Genetics & Botany

What role do genes play in regards to flavour. This page will be updated as new information is received.  Last edited July, 2019.  

+ Varieties

First, let's try and make sense of the different ways T. cacao is organized. We will discuss variety, cultivar, heirloom, hybrids, and clones. Understanding how genetics impacts flavour is easier when we understand the ways in which we categorize cacao according to genetics.

The species name for our chocolate making tree is Theobroma cacao. Within this species are many subspecies or varieties. A variety is generally accepted to be a wild, genetically unique group within a species that produces sexually . It’s often very difficult to know which varieties are wild, as they may have been shaped by human involvement thousands of years ago, and only today appear to be wild. However, advances in genetic research has allowed researchers to analyze and trace the various genomes, which tell their own story of where they came from.

For centuries, there has been a great deal of debate and confusion over the nomenclature of cacao varieties. In the 21st Century, genetic research has brought forth more clarity to how we categorize the different varieties. In 2008, J. C. Motamayor of Mars Inc. published an article that suggested 10 groups or clusters of genetically similar cacao grups that could be used within the industry as wild varieites. Many have accepted this, but not everyone. For our purpose here, will will use his suggestions to refer to wild varities of cacao. The list of ten T. cacao groups or clusters suggested my Motamayor include:

  • Maranon
  • Curaray
  • Criollo
  • Iquitos
  • Nanay
  • Contamana
  • Amelonado
  • Purus
  • Nacional
  • Guiana

All these varieties were discovered in Central and South America, mainly within the Amazonian region, which is the native area where T. cacao evolved. Of course, this is likely not an exhaustive list. As more genetic research and fieldwork pours in, these suggestions will be challenged. I will aim to keep you updated on these changes as they occur.

Older literature, and even current literature, still refers to the old nomenclature of varieties. This includes Criollo (the fine cacao), Forastero ("bulk cacao"), and Trinitario (a hybrid of the previous two). Many still categorize chocolate within these 3 cateories.

Forastero is now considered an umbrella term for many varieties, often associated with poor flavour. The varieties of cacao taken to West Africa decades ago to develop the cacao industry there (which produces 75% of the worlds cacao) appear to be of the Amelonado variety, but still referred to as Forastero (However, it doesn't mean all Amelonado genotypes are of poor quality). Even in new research articles, scientists still use the old nomenclature, and it will take more time and understanding until the more updated terms become common use. This is often due to outright ignorance of their existence, or the confusion surrounding them, which in my opinion keeps even scientists from using them. Today, what is still termed forastero is generally bulk cacao that is very bitter, dry, and contains little or no favorable aromas. It’s used because the trees are hearty and produce bigger pods, making it more profitable to grow.

Criollo is considered a variety, but is it really a wild variety? It’s believed to be a variety developed by Mesoamericans. It’s generally a very fragile variety, prone to disease and low yields, but also produces fruit and seeds of favorable aromas. There appears to be no genetically pure criollo today, since most of it has been cross bred with other varieties to produce more hearty trees. Much of the criollo strains today appear to be coming out of Venezuela but also some from Mexico as well. The criollo cacao is often associated with less bitterness, and notes of cream and butter.

Trinitario is believed to be a hybrid that occured in Trinidad & Tobago. Forastero was brought in to replace a dying criollo population of trees, and hybridized into a type of cacao that had better aroma qualities than forastero, but stronger than the criollo. Trinitario is not a variety. They have been crossed back into other varieties, and so there's really no true trinitario type. Trinitario is grown worldwide, from South America to South East Asia. Trinitario is more or less a mutt of cacao, and depending on where in the world is grows and what genetics it contains, it can vary greatly in appearance and quality.

Nacional is a variety that is said to be rediscovered in the 21st Century. One hundred years prior, it was belied this variety was wiped out from the Amazon due to disease. However, some researchers discovered that some trees still existed in the North West Amazon in Ecuador, and is now being grown there and sold to those willing to pay a premium for it. Nacional cacao is associated with floral-like aromas, and is known to have a very low level of bitterness.

As more research and education spreads throughout the cacao and chocolate industry, expect to see different names of varieties on the packages of your fine chocolate bars.

Also keep in mind that how variety is defined here is not always how the term is used. You will read more about the different types of cultivars which exist. Sometimes these cultivars are also referred to as varieties, but not in the "wild variety" way described here.


+ Cultivars

From the varieties come cultivars. Cultivars are a unique genetic type often created by humans within the confines of cultivation, although they can be brought in from the wild as well (I know it gets confusing!) Here we will reserve the term “variety” to be associated with a genetic wild variety, the 10 mentioned above. Every other type which is not a variety will be considered a cultivar. Cultivars can be heirlooms, a hybrid, or a clone.


These are cultivars which meet cultural specifications, not scientific ones. They are singled out for their specific traits, which are favoured by the locals from where it was first cultivated, and reproduce via sexual propagation. Heirloom isn’t necessarily synonymous with high quality or best flavour, although it does suggest it.

Depending on the country, the term heirloom has flexible definitions. Generally speaking, they should be associated with a specific geographical region, naturally reproduce sexually (from insects pollinating the trees, not human interaction or cloning), have reproduced over multiple generations, and produce offspring with consistent characteristics.

It’s these characteristics which the locals agree upton to be considered heirloom. However, just because a cultivar is termed heirloom (and you will see this on chocolate bar packaging today) it doesn’t necessarily mean it is without a doubt of high quality. Nor does it mean the chocolate made from it will taste incredible. However, people don’t often put so much time and effort into a heirloom that is of low quality, so heirloom does suggest higher quality. Just be aware that it’s a term that can be misused in marketing, and that just because it is classified as heirloom by some organization or country, doesn't necessarily mean the flavour will blow your mind. Even if the heirloom is of high quality, what the maker does or doesn't do will greatly impact the flavour as well.


A combination or recombination of two or more varieties or cultivars. These also must produce sexually, although a hybrid may be hand pollinated as well (where a farmer artificially rubs the pollen from one tree onto the stamen of a flower on another tree). Hybrids are often unpredictable, as they carry a mix of genetic information that isn’t necessarily constant from generation to generation. Very specific hybrid genotypes which are deemed highly deseriable are often cloned.


I’m not talking about test tube Frankenstein trees. We're not talking about genetically modified organsims in this case.

A clone is a cultivar that is achieved through non sexual propagation, where the parent tree is identical to the daughter tree. This is most often accomplished through grafting. A portion of the parent tree is removed, and grown separately into a genetically identical tree. Propagation this way allows the farmers to consistently produce cacao with the exact same characteristics. However, this lack of genetic diversity within the farm can result in a great deal of damage to the entire crop if they were to encounter disease or pestilence.

Many cacao trees which are grown on farms today are most often clones, with specific code names, such as EET 62, ICS 1, U 43, CCN 51, PA 169. Private or government run agricultural agencies will manage or maintain these clones. These clones are then purchased by local cacao growers or sent to other countries for study or to incorporate into the local genetic pool of cacao.


+ Importance of nomenclature for the consumer

Are these terms important? Do they determine flavour or quality? To the grower and the chocolate maker, they are important. For the grower, understanding and clarifying what genetics they are dealing with helps them sustain high quality cacao. For the maker, choosing flavourful cacao beans is crucial to their work.

However, to the consumer, these terms have more to do with marketing than distinguishing flavour or quality. What a chocolate maker does with the finest heirloom cacao is more important than you knowing what cacao they are using. Certain varieties become synonymous for quality and flavour, and begin to be marketed for the cachet meaning they hold. Although variety and cultivar does affect flavour, it's only one aspect, and shouldn't be the deciding factor in determining your choice.

Let's look at this way. A musician can own the most sought after fiddle on the market, but if they don't execute, if they are not skilled enough, what they create will not do the fiddle justice. Does one listen to music based on what instrument the musician is using, or what music then can create with it? The same goes for chocolate. Genetics (variety, cultivar, etc.) is important, but shouldn't outweigh the many other aspects of the process of chocolate that greatly determine flavour. What the farmers and chocolate makers do with their cacao has a huge impact on final flavour.

That said, genetics is important to flavour. The genetics of a tree will dictate the molecules within the seed, that is, the building blocks of future flavour. If a certain genetic makeup contains building block molecules that will lead to very bitter, bland, cacao, there isn't much a farmer or maker can do to make it taste incredible. On the other hand, if the cacao contains the building blocks that will allow for incredible floral and nutty aromas if they are manipulated properly by the farmers and makers, then it's important to obtain such cacao.

As well, the more information about the cacao the maker puts on the label, the more transparent they become, and the more trustworthy. It suggests they take their chocolate making seriously, and value quality. However, marketing is full of misinformation as well, and mislabelling does occur.


+ The Fruit

Current research points to the flavour of the fruit also impacting the flavour of the cacao bean. The flavour of the fruit is associated with the variety or cultivar it grows from. Read this study about how fine flavour cacao came from delicious fruit, while bulk cacao came from trees that also produced acidic and bland fruit. There is certainly a relationship here.

Some have experimented by adding the fruit of other plant species (such as soursop), and mixing it in with the fermenting cacao seeds. They determined that aromas found within the added fruits were also found within the post fermented cacao beans. Adding other fruits to the fermentation mass altered the aroma profile of the cacao, which altered the aroma profile of the chocolate.

If the genetics dictates the flavour of the fruit, and the fruit alters the aroma profile of the seed, then it appears that genetics has direct and indirect impacts on the flavour of our chocolate.

+ The Seeds

This section will go into a little more detail as the "variety" section above.

Cacao seeds from the amelonado variety are known to be more astringent due to having a greater amount of bitter polyphenols. Amelonado, which is a variety that was often found under the umbrella term "forastero", was taken from Bahia Brazil to West Africa in the 20th Century, and now makes up the bulk of the cacao grown in the world. It's favorable mostly for yield (larger pods, more seeds, less susceptible to disease), but not often known for quality or flavour.

Criollo is understood to be a variety that was cultivated by the Mesoamericans for centuries if not millennia, and is often much less astringent. It's known to carry many favorable aroma compounds. It's also the most sought after cacao within the fine chocolate industry. It's seen as the finest of the cacao varieties because of the potential aromas one can create with it. However, don't expect all "criollo" made chocolate to taste better than another variety. As well, criollo today is a term used for cacao that is most often not pure criollo, but criollo mixed with another variety such as amelonado.

Nacional is known to be much less astringent as well, often with nutty or fruity notes to it. Nacional boasts cacao with a high ratio of blonde seeds, which make it less astringent as well. It's a variety that was thought to be wiped out from disease, but is now making a comeback.

Other varieties have not become as mainstream yet, but Maranon is also known to produce very flavourful chocolate as well.

The cultivation of different varieties depends on their demand. The more chocolate makers seek to experiment and use different cultivars, the more likely they are to be worth producing.


+ The Metabolism

Genetically unique trees will metabolize differently, uptake different minerals and interact differently with their environment, which will also impact the flavour of the cacao bean. Not even just within a population, but within individuals that have specific genetic traits. Trees grown within the same plantation will uptake different levels of minerals and nutrients. Not enough research has been done to connect the levels of minerals to the flavour of cacao beans or chocolate, and so we can't yet state that for instance higher amounts of iron will produce a certain flavour. However, from understanding mineral uptake in other species of botanicals, and how that affects flavour, we can begin to look for similar patterns in cacao.

+ Conclusion

Understand that although genetics is important, there is very little transparency or clarity when it comes to cacao genetics today, even within the smaller scale bean to bar world. The reason I mention this is to not make the variety or type of cacao the greatest deciding factor on the value of your chocolate bar.

There are differences between varieties and cultivars, but placing your judgement of the chocolate based on this alone is very misleading. Chocolate is a highly processed food. Not highly processed in the sense of preservative laden and artificial ingredients, but that it goes through many steps until the final product is achieved.

Therefore, although the genetics of the tree is the first player in the game of flavour, there are many other factors later that determine the final flavour of the chocolate bar. A chocolate should be judged not only on the "variety" but also on other more important factors as well, which include what the farmers and especially the makers do with the cacao.