The Near Extinction of Ancient Nacional Cacao | To'ak Chocolate
History + Culture 12 min read

The Near Extinction of Ancient Nacional Cacao

Jerry Toth

14th of June 2018


The legendary Ecuadorian cacao variety called “Nacional” traces its genetic lineage back to the first-known cacao trees domesticated by humanity, about 5,300 years ago. After achieving global fame in the nineteenth century, the variety was nearly lost in the twentieth century. As recently as 2009, pure Nacional cacao was believed to be extinct. In the valley of Piedra de Plata we found one of the last surviving groves of 100% pure Nacional cacao—which geneticists refer to as Ancient Nacional.

This article takes a deep dive into the history of Nacional cacao and a closer look at its complicated genetic status today. It discusses the difference between 100% pure Nacional, which is currently on the brink of extinction, versus the relatively more common Nacional hybrids, which are also in rapid decline. The article also introduces the work we're doing to keep this hallowed cacao variety alive and usher forth a new era of heirloom Nacional cacao in Ecuador. 

To jump ahead to our conservation work, you can read The Genetic Bank of Ancient Nacional Cacao


1. The Origins of Cacao

The earliest evidence of cacao used by humanity dates back to 3300 BC in Ecuador, in the area now called Zamora Chinchipe.[1] From this general area it is believed that cacao then migrated to coastal Ecuador and presumably traveled northward as far as Mexico.[2] The broader pre-Colombian migration pattern of cacao is still not fully understood and is beyond the scope of this present article. My intention here is to focus specifically on the past, present, and future of the cacao variety that is now known as "Ancient Nacional."

As cacao acclimated to diverse localities throughout the Americas, distinct varieties began to form on the genetic family tree. For most of the 20th century, cacao was roughly divided into three overly-expansive genetic groups: Forastero, Criollo, and Trinitario. In 2008, Juan Carlos Motamayor classified cacao into ten genetic clusters. Motamayor’s system is “a new classification of cacao germplasm into ten major clusters, or groups” which “maintains the terms used to identify the traditional cultivars Amelonado, Criollo, and Nacional, and separates highly differentiated populations within what was previously classified as the Forastero genetic group.”[3]

Nacional cacao pod from the valley Piedra de Plata in Manabí, Ecuador. Held in the hand of Servio Pachard.

The genetic researchers at the USDA Agricultural Research Service (USDA-ARS) use a similar classification system, albeit organized in a slightly different way, which their genetic researcher Dr. Dapeng Zhang was kind enough to explain to me. The USDA-ARS uses the term Ucayali/Scavina in place of what Motamayor calls Contamana, the term Parinari in place of what Motamayor calls Marañon, and the term Iquitos Mixed Calabacillo (IMC) in place of what Motamayor calls Iquitos. The USDA-ARS also describes an additional genetic cluster, called Boliviano, that is not included on Motamayor’s list.

An integrated list of the USDA-ARS and Motamayor classification system looks like this:

• Amelonado
• Boliviano
• Contamana aka Ucayali/Scavina
• Criollo
• Curaray
• Guiana
• Iquitos aka Iquitos Mixed Calabacillo (IMC)
• Marañon aka Parinari
• Nacional
• Nanay
• Purús

These eleven “genetic clusters” are considered the primary varieties of cacao. It should be noted that Ucayali/Scavina, Curaray, IMC, Parinari, Nanay, and Purús are often collectively referred to as “Upper Amazon Forastero.” Amelonado is sometimes referred to as “Lower Amazon Forastero.”[4]

In addition to these primary cacao varieties, there are countless hybrids and cultivars. Trinitario, a term commonly used in the past, is a hybrid of Amelonado, Upper Amazon Forastero, and Criollo.[5] The genetic composition of CCN-51, which is fast becoming the dominant cacao cultivar in spite of its poor flavor reputation, is 45.4% IMC, 22.2% Criollo, 21.5% Amelonado, 3.9% Contamana, 2.5% Purús, 2.1% Marañon, and 1.1% Nacional.[6]

2. The Story of Nacional

All of the above cacao pods were harvested from trees in Piedra de Plata that were DNA-tested. One of them is 100% pure Nacional; the rest of Nacional hybrids. From left to right, their respective Nacional percentages are: 100%, 82%, 80%, 72%, 60%, 49%, and 40%.

It is safe to say that Nacional is the most storied of the world’s cacao varieties. It is also the most enigmatic. Until recently, there was no consensus as to its origins. In 2012, a study by Loor Solorzano effectively conducted a paternity analysis of Nacional cacao. It compared the genetics of Nacional cacao trees from coastal Ecuador to 169 wild and cultivated cacao accessions from throughout South and Central America. The highest genetic similarity was found between Nacional cacao and wild cacao genotypes from the same area in Ecuador believed to be the origin of cacao, in Zamora Chinchipe. The results of this study thus suggest that Nacional cacao is the direct descendent of the earliest known cacao trees used by humanity.[7]

The prevailing hypothesis is that traders transported the ancestors of Nacional cacao from the upper Amazonian forests near Zamora Chinchipe to the upper Guayas River basin, in coastal Ecuador, during ancient times. Loor Solarzano also suggests the probability that the genetic divergence of Nacional cacao was the result of selection pressure in favor of its characteristic aroma. “From this standpoint, the specific aromatic flavour of chocolate produced from Nacional cocoa beans, which can already be detected on the bean pulp, even without a fermentation step, could have been one of the criteria used by the primitive human communities to choose the cocoa mother tree for further seed sowing. Indeed, it is possible that travelling merchants transporting cocoa pods along the roads used the fresh pulp only for their own refreshment and nutrition, but without consuming the cocoa beans, thereby introducing the cocoa tree into a new environment.”[7]

Map of the historical "Arriba" cacao growing region illustrated by Carl Schweizer, co-founder of To'ak.

Fast forward a few millennia. During Francisco Pizarro’s first voyage along the Pacific coast of South America in 1526, the Spaniards found evidence of small plantations of cacao trees in what is now coastal Ecuador. In the 1600s, colonists began reproducing these native cacao trees in the upper Guayas river basin along its primary tributaries—namely, the Daule and Babahoyo rivers and smaller tributaries. Cacao from this region later acquired the name “Arriba,” derived from the geographical description “rio arriba” (meaning, “up river”). Ancient Nacional is the genetic variety that this nineteenth-century term referred to.[8]

Over the course of the eighteenth and nineteenth centuries, cacao cultivation continued to expand in coastal Ecuador. Cacao from this region became globally renowned for its strong floral aroma and desirable flavor characteristics, such that “Arriba” became the most prestigious denomination of origin in the international cacao trade. Ancient Nacional cacao had reached the pinnacle of the market.[9]

As of the 1890s, Nacional was the only cacao variety planted in coastal Ecuador. The landscape began to change in the beginning of the twentieth century with the back-to-back arrival of frosty pod disease (Moniliophthora roreri) in 1916 followed by witches’ broom disease (Moniliophthora perniciosa) in 1919.[8]

The arrival of these two fungal diseases marked a great disruption in the Nacional family tree. Between 1916 and 1932, Ecuadorian cacao production decreased by 77%.[10] As Nacional cacao suffered widespread casualties during the 1920s, foreign cacao seeds began to make their entrance, and a century of hybridization ensued.[8]

Monilla - Cacao

The predominant cacao cultivars that infiltrated Ecuador during this period were from the “Trinitario” family, which arrived to Ecuador via Venezuela. Many of these Trinitario cultivars probably originated in the so-called “Pound Collection” in Trinidad, which is responsible for much of the genetic configurations of cacao found throughout the world today. As stated previously, Trinitario cacao is a mix of Upper Amazon Forastero, Amelonado, and Criollo cacao. This particularl blend of genetics proved to be relatively resistant to disease while still maintaining “fine flavour” characteristics.[11]

Chocolate produced from Trinitario cacao is generally known for a fruity flavor profile. Nacional, on the other hand, is celebrated for its floral aroma and its flavor complexity. Starting as early as the 1920s, and accelerating through the 1940s, Trinitario cacao seeds were interplanted with Nacional trees that survived the outbreak of disease in the 1920s. The new arrivals then sexually paired with Nacional cacao through open pollination, producing offspring of mixed descent. Nacional was still the predominant variety of this next generation, but now Upper Amazon Forastero, Amelonado, and Criollo genetics were mixed in. For the most part, this new genetic admixture continued to reproduce via open-pollination for the next several decades.[8]

This pattern prevailed until the 1970s, when Ecuador’s agricultural research institute (INIAP) released its first generation of higher-yield clones from Nacional trees bred with foreign cacao varieties—again, usually a mix of Upper Amazon Forastero, Amelonado, and Criollo. A second generation of INIAP clones was released in 2009. The most recent edition of INIAP clones (EET-800 and EET-801) was released in October of 2016.[12]

As Nacional cacao hybridized over the course of the past hundred years, its aroma and flavor profile has likewise evolved. It should also be noted that the soil on which Nacional cacao is grown has also changed over the centuries, as a consequence of long-term cultivation. Therefore it is probable that a 120-year old pure Nacional cacao tree today would present somewhat different organoleptic properties than pure Nacional trees in 1900, even though they are genetic equals. It’s important to remember that the intrinsic flavor profile of cacao is a function of genetics and terroir. And then when cacao is converted into chocolate, the human factor comes into play.

Nevertheless, the signature aroma and flavor profile of Nacional can still be found in the old-growth cacao trees growing in places like Piedra de Plata. Some of the same organoleptic properties are also present in the Nacional hybrids, where the floral components of Nacional and the fruity components of Trinitario both find expression. Today, when most dark chocolate makers put the word “Nacional” on their label, they are almost always referring to Nacional hybrids, as opposed to pure Nacional. In Ecuador, the term used to describe Nacional hybrids is "Complejo Nacional." This is not the same thing as pure Nacional.

By the dawn of the twenty-first century, 100% pure Nacional was believed to be extinct.[13] In 2009, Ecuador’s agricultural institute (INIAP) collected DNA samples from 11,000 cacao trees throughout Ecuador, and only six of these trees (out of 11,000 samples) were 100% pure Nacional. That’s a mere 0.05% of the cacao trees that were analyzed.[14] In addition to these six trees in Ecuador (located in two farms, La Gloria and Las Brisas), a third site with pure Nacional was discovered in the Marañon valley in northern Peru, close to the Ecuadorian border. Aside from these three sites, it was commonly believed that pure Nacional no longer existed prior to our DNA analysis in Piedra de Plata.

Meanwhile, as this current century has worn on, a new threat to pure Nacional has emerged, under the name CCN-51. Roundly criticized for its flavor but spectacularly productive, CCN-51 is a new high-yield cultivar that is rapidly taking over cacao production in Ecuador and throughout the world. Many of the pure Nacional trees that survived the past century were cut down and replaced by CCN-51. Nacional hybrids, which are still somewhat widespread in certain parts of Ecuador, are also rapidly disappearing in the face of CCN-51.[15]

A drive through the Ecuadorian provinces of Guayas, Los Rios, and Esmeraldas paints a dire picture of the current situation, where CCN-51 monocultures are increasingly monopolizing cacao production. It has been estimated that 90% of the cacao trees that have been newly planted in Ecuador in the last 20 years are CCN-51.[16] The province of Manabí, owing to its rugged terrain, which does not lend itself well to monocultures, is the last major stronghold of pure and hybridized Nacional in Ecuador.


3. Piedra del Plata

The valley of Piedra de Plata in the province of Manabí—the heartland of Ecuadorian cacao country and the last true stronghold of Nacional.

Our relationship with Piedra de Plata began in 2013, thanks to Servio Pachard. Piedra de Plata is a valley deep in the hills of the province of Manabí. It was disconnected from the rest of the country by road until the 1990s. What attracted us to Piedra de Plata was the unusually high presence of cacao trees that were over one hundred years old, meaning that some of these trees were born before the arrival of Witches’ Broom and Frosty Pod disease in the early 1900s. It also meant that these same trees somehow survived the epidemic and have therefore proven resistant to these diseases.

We hypothesized that some of these old-growth cacao trees in Piedra de Plata must be 100% pure Nacional. In addition to their old age, many of these same trees also exhibited the primary indicators of pure Nacional—namely, yellow fruit pods (as opposed to red or reddish); elliptical in shape (as opposed to oblong or orbicular); attenuate apex (as opposed to acute or obtuse); moderate basal constriction of the pod (as opposed to no constriction or pronounced constriction); and reddish stamen pedicels of the flowers (as opposed to unpigmented pedicels).[17]

In 2015, we put this hypothesis to the test. In partnership with the Heirloom Cacao Preservation Fund (HCP), we analyzed the DNA of 47 trees in Piedra de Plata. We collected the leaf samples under the direction of Freddy Amores, the director of cacao research at Ecuador’s leading agricultural institute (INIAP). The genetic analysis was performed by Dr. Lyndel Meinhardt and Dr. Dapeng Zhang at the USDA-ARS genetic lab in Maryland.

Before the results were compiled, we were politely warned by numerous people within the industry that we would probably not find any pure Nacional cacao trees in Piedra de Plata or anywhere else. Fortunately, this was not the case.

Out of a broad sampling of 47 cacao trees in Piedra de Plata, in which trees of all ages and characteristics were analyzed, nine trees proved to be 100% pure Nacional. In total, 31 of the 47 trees were at least 70% Nacional, and only five of the 47 were less than 50% Nacional.


4. The Genetic Bank

Seedling grafted from a pure Nacional tree from Piedra de Plata, now living in the Genetic Bank of the Jama-Coaque Reserve.

The term used by the USDA-ARS genetic lab to describe 100% pure Nacional is “Ancient Nacional.” These nine trees, when added to the six pure Nacional trees that INIAP discovered in 2009, add up to only fifteen DNA-verified “Ancient Nacional” cacao trees in all of Ecuador. To make matters more precarious, all of these fifteen trees are estimated to be over one hundred years old, which is typically the end of a cacao tree’s lifespan. There was a very real fear, among all parties concerned, that these trees can and most likely will die any year now.

The Genetic Bank is our way of keeping this ancient variety of cacao alive. We took cuttings from each of the Ancient Nacional trees in Piedra de Plata and grafted them onto seedlings, which we then transplanted in a nearby protected area. To do so, we partnered with Third Millennium Alliance (TMA), a nonprofit rainforest conservation foundation based in Ecuador.

TMA manages the Jama-Coaque Ecological Reserve, located in the same province (Manabí) as Piedra de Plata. TMA also represents a key part of the origin story of To’ak. I co-founded TMA in 2007, along with Isabel Dávila and Bryan Criswell. The Jama-Coaque Reserve is where I first started cultivating cacao and making chocolate. Not surprisingly, To’ak and TMA have always been informally aligned. The Genetic Bank was the perfect opportunity to formalize that partnership and work together toward a common goal.

The third member of this partnership is the regional university, Escuela Superior Politécnica de Manabí (ESPAM). To’ak provided the genetic data and field work associated with sourcing the cuttings and ESPAM provided technical assistance with grafting the cuttings onto seedlings. TMA provided a plot of land in the Jama-Coaque Reserve to receive the seedlings, along with all labor and expertise associated with transplanting the seedlings and managing the cultivation of the trees over the course of their lives, under my direction.

With the help of Paul Cedeño and his team at ESPAM, we took cuttings from each of the nine trees and grafted them onto seedlings. Specifically, we produced 21 clones of each of the pure Nacional trees, producing a total of 189 pure Nacional seedlings.

These young trees are now successfully planted in a special parcel of the Jama-Coaque Reserve. We call it the “Noah’s Ark” of Ancient Nacional cacao. Within three years, these young trees will provide enough cuttings to reproduce up to 5,000 pure Nacional seedlings each year, which will then be distributed to any local cacao grower who wants to help save this historic variety from extinction.

For a more detailed account of our conservation work and our vision for the future of Nacional cacao, you can read The Genetic Bank of Ancient Nacional Cacao.




[1] Lanaud C., Loor Solórzano R.G., Zarillo S. & Valdez F. (2012) Origen de la domesticación del cacao y su uso temprano en el Ecuador, Nuestro Patrimonio 34: 12-14.

[2] Zhang D. & Motilal L. (2016) Origin, Dispersal, and Current Global Distribution of Cacao Genetic Diversity. Cacao Diseases: A History of Old Enemies and New Encounters. Eds. Bailey, B.A.; Meinhardt, L.W. Springer, 2016.

[3] Motamayor J.C., Lachenaud P., Da Silva e Mota J.W., Loor Solórzano R.G, Kuhn D.N., et al. (2008) Geographic and genetic population differentiation of the Amazonian chocolate tree (Theobroma cacao L.) PLoS One, 3 (10): e3311 (8p.).

[4] Bekele, Frances & Butler, David & Bidaisee, Gillian. (2008). Upper Amazon Forastero cacao (Theobroma cacaoL.) 1: An assessment of phenotypic relationships in the International Cocoa Genebank, Trinidad. Tropical Agriculture (Trinidad). 85.

[5] Yang, JY. Scascitelli, M. Motilal, LA. Sveinsson, S. Engels, JMM, Kane, NC et al (2013). Complex origin of Trinitario-type Theobroma cacao (Malvaceae) from Trinidad and Tobago revealed using plastid genomics. Tree genetics & genomes 9 (3), 829-840.

[6] Boza E., Motomayor J.C., Amores F., Cedeño-Amador, Tondo C., et al. (2014) Genetic Characterization of the Cacao Cultivar CCN 51: Its Impact and Significance on Global Cacao Improvement and Production, JASHS 139: 2219-229.

[7] Loor Solórzano R.G., Fouet O., Lemainque A., Pavek S., Boccara M., et al. (2012) Insight into the Wild Origin, Migration and Domestication History of the Fine Flavour Nacional Theobroma cacao L. Variety from Ecuador. PLoS ONE 7(11): e48438. doi:10.1371/journal.pone.0048438.

[8] Loor Solórzano R.G., Risterucci A.M., Courtois B., Fouet O., Jeanneau M., et al. (2009) Tracing the native ancestors of modern Theobroma cacao L. population in Ecuador. Tree genetics and genomes, 5 (3): 421–433. [20100330]. doi:10.1007/ s11295-008-0196-3.

[9] Preuss P. (1901) Expedition nach Central- und Sudamerika 1899/1900. Kolonial-Wirtschaftlichen Komitees, Berlin.

[10] Benites Vinueza L. (1950) Ecuador: drama y paradoja. [1. ed.] México: Fondo de Cultura Económica.

[11] Zhang D. & Motilal L. (2016) Origin, Dispersal, and Current Global Distribution of Cacao Genetic Diversity. Cacao Diseases: A History of Old Enemies and New Encounters. Eds. Bailey, B.A.; Meinhardt, L.W. Springer, 2016.

[12] Amores, F. (2002) Ecuador: Pasado, Presente y Futuro de la Investigación en Cacao. Estación Experimental Tropical Pichilingue, INIAP.

[13] Haggarty, E. (2011, January 13) Chocolate made from “extinct” beans comes to Canada. Toronto Star.

[14] Christian, M. (2012, December) The Mother ‘F’ Tree. C-Spot.

[15] Nieburg, O. (2016, August 9). CCN-51: Cocoa’s shining light or risky monocrop? Confectionary News.

[16] Amador, SC. (2011, April). La Revolución del Cacao CCN-51 en el Ecuador. CMAA International Cocoa Conference. Nassau, Bahamas.

[17] Soria JV and Enriquez GA. (1988). International Cacao Cultivar Catalogue. Technical Bulletin #6. Centro Agronómico Tropical de Investigación y Enseñanza (CATIE): Costa Rica, 14.