Cocoa is an economically important product in Colombia but is little studied. On-farm germplasm evaluations allow the selection of superior genotypes for propagation and distribution throughout the country. The present study analyzed 68 cocoa samples from Antioquia and five reference materials using 96 single nucleotide polymorphism (SNP) markers. The 12 most outstanding materials were selected according to physical, chemical, and sensory characteristics. Primary coordinate analysis demonstrated that most samples were hybrids derived from five original germplasm pools, including Creole, Amelonado, and three Upper Amazon Forastero cocoas. The integral profile of the 12 selected materials was classified as fine aroma (3), Forasteros (3), and Trinitarios (6). Three factors were identified that best explained the classification of samples: type of variety, functional properties, and quality.