A new genetic analysis of hundreds of cacao trees representing traditional Amazonian varieties grown on farms across Peru has revealed four previously unidentified, genetically distinct groups. Lambert Motilal with colleagues from the Cocoa Research Centre, The University of the West Indies, and Martha S. Calderon and Danilo E. Bustamante, with their colleagues from the Universidad Nacional Toribio Rodríguez de Mendoza, partnered to explore Peru's untapped cacao diversity. They present these findings in the open access journal PLOS One on July 6, 2026.
Cocoa beans from cacao trees underpin the world's multibillion-dollar chocolate industry. In Peru, the eighth-largest cocoa producer, more than 80,000 farming families relied on cocoa cultivation as of 2024. Many Peruvian farms grow wild and semi-wild cacao varieties that have not been significantly altered by such means as selective breeding or genetic engineering. Prior research suggests that indigenous cacao trees farmed in Peru and other countries can be categorized into 10 groups, based on their genetic similarity to each other. Individual trees may represent a pure group or a combination of various groups.
However, more recent research has challenged the 10-group framework, and few studies have focused specifically on Peru. To improve understanding, Motilal, Calderon, Bustamante and colleagues analyzed the genetic diversity of 390 wild and semi-wild cacao trees grown on indigenous farms in various regions across Peru. Specifically, they analyzed single-nucleotide polymorphisms (SNPs)—single-letter differences between individual trees' DNA code that help to illuminate their genetic diversity and relationship to each other, enabling categorization into genetically similar groups.
The analysis revealed four previously unidentified genetic groups, in addition to the 10 already known. Some of the analyzed trees fell into one pure group, while others were mixes. The researchers found that different regions of Peru had their own, distinct genetic "signatures," highlighting fine-scale geographic differences in the genetic composition of farmed cacao trees.
Two of the four groups have ancestry that suggests they might produce especially high-quality, well-flavored beans, according to the researchers.
The analysis also helped to clarify the ancestry of a particular cacao variety known as CCN 51, which was deliberately cultivated for high yield and disease resistance and is increasingly economically important.
These findings could be leveraged for conservation efforts and also to improve the Peruvian cacao industry, the researchers say.
The characterization of the four new groups suggests that Peru harbors unique genetic resources that could be explored for valuable traits for the cacao and chocolate market.
The authors add: "Our research reveals that while Peru's cacao trees share a common genetic thread across the country, each region harbors a unique genetic signature and we've successfully pinpointed four entirely new cacao lineages. This blueprint not only reshapes our understanding of Peru's genetic landscape but provides a tangible new resource for conservation and the fine flavor chocolate industry."
"One of the most rewarding aspects was working directly with Indigenous on-farm trees across eight vastly different departments, from the Amazonas lowlands to the Andean foothills. It was eye-opening to realize that these invaluable genetic treasures weren't locked away in a lab. They were literally growing in farmers' backyards, waiting to be characterized and valued for the premium market."
Author interview: https://plos.io/4g8BXg9
In your coverage, please use this URL to provide access to the freely available article in PLOS One: https://plos.io/4eEIAnM
Citation: Motilal LA, Calderon MS, Bustamante DE, Gopaulchan D, Tineo D, Márquez-Romero FR, et al. (2026) Genetic structure of traditional cacao reveals four new genetic lineages in indigenous Amazonian sites in Peru. PLoS One 21(7): e0351690. https://doi.org/10.1371/journal.pone.0351690
Author countries: Trinidad and Tobago, Peru, UK.
Funding: This study was supported by the Consejo Nacional de Ciencia, Tecnología e Innovación Tecnológica (CONCYTEC) through FONDECYT (Contract N 026-2016 to M.O.) for the project "Círculo de Investigación para la Innovación y el fortalecimiento de la cadena de valor del cacao nativo fino de aroma en la zona nor oriental del Perú (CINCACAO)", PROCIENCIA (PE501079652-2022-PROCIENCIA to D.E.B.) for the Project MiCroResi, and Universidad Nacional Toribio Rodríguez de Mendoza de Amazonas through Vicerrectorado de Investigación (VRIN to D.E.B.). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
