Technical Abstract: The tropical tree crop Theobroma cacao L. is grown commercially for its beans, which are used in the production of cocoa butter and chocolate. Although the upper Amazon region of South America is the center of origin for cacao, 70% of the world’s supply of cocoa beans currently comes from small farms in Africa where harvested beans serve as the primary cash crop. While cacao breeding programs in producer nations continue to serve as an invaluable source of improved planting material, modern marker-based breeding is difficult to perform due to the lack of genotyping facilities in these areas. We describe a SNP marker-based method to successfully genotype cacao plants under conditions similar to those found in most cacao producing areas. This field SNP assay forgoes expensive realtime machines and automated sequencers, in favor of less expensive standard thermocyclers and a microplate reader. The assay was tested under field conditions by planting open pollinated seeds of seven pods from three different maternal plants. The resulting 171 seedlings were successfully genotyped with 19 SNP markers representing 13 loci. The ability to use temperature stable reagents and rapid DNA extraction methods is also explored. Additionally, by examining the seedling genotypes from the SNP markers and 13 additional microsatellite markers we investigate whether seeds in a pod are the result of single or multiple pollination events. This simple, effective method to genotype cacao seedlings in the field should allow for more efficient resource management in breeding programs, and is currently being implemented in Ghana.