Cacao tree (Theobroma cacao L.) is the source of raw ingredients for the chocolate confectionary industries. Recent progress in cacao genomic resources development has led to the discovery of new Single Nucleotide Polymorphisms (SNP) markers, and to their application in high-throughput genotyping for cacao germplasm characterization. Fluidigm SNPtype Assays, combined with Dynamic Array Integrated Fluidic Circuits (IFCs), enable rapid and accurate high-sample throughput for low- to mid-multiplex SNP genotyping. As a proof of principle, we selected 48 previously characterized SNP markers, distributed across all 10 chromosomes, and designed a SNPtype genotyping panel for cacao germplasm identification. We demonstrated rapid, reliable, and low-cost genotyping of cacao accessions representing diverse genetic populations. Genomic DNA samples were extracted from fresh leaves, dry leaves, and fermented/dry beans using a Qiagen® DNeasy Plant Kit. Cacao DNA samples¾known to be challenging for PCR-based applications due to the presence of high levels of polysaccharides and polyphenolic compounds¾were successfully genotyped using our Specific Target Amplification (STA) protocol, achieving outstanding data quality (>99.32% auto call rates). These findings demonstrate a robust and simple genotyping tool for management and improvement of cacao germplasm, and will be of interest to broad groups of scientists using SNP markers for germplasm characterization.