Cacao (Theobroma cacao L.) is an important Neotropical crop originating in South America and dispersed by European explorers, arriving in Madagascar in the late 19th century. Although Madagascar is an important producer of cocoa for the premium chocolate market, the varietal composition and genetic diversity in cacao germplasm from Madagascar, especially in traditional cacao farms, remains unknown. A total of 190 cacao accessions, including 40 farmer accessions collected from traditional cacao farms in Madagascar, and 150 accessions representing seven reference cacao populations, were analyzed using Single Nucleotide Polymorphism (SNP) markers. Multivariate analysis and Bayesian stratification resulted in the clustering of the 40 farmer accessions into three groups: Criollo, Amelonado and Trinitario. These three traditional varieties were commonly cultivated in tropical America in the 18th century, but most of them have been replaced by improved varieties. The present study demonstrated that Madagascar is distinctive in that all three traditional cacao varieties, Criollo, Amelonado and Trinitario, are still maintained on-farm for cocoa production, as in Mesoamerica and the Caribbean several hundred years ago. Results from the present study are significant in terms of understanding the early dispersal of cacao from tropical America and Asia to Africa, in addition to the well-documented route from Brazil to São Tomé & Príncipe. The results also provide new information for planning future conservation and utilization of cacao germplasm in Madagascar.