Phytophthora megakarya is an aggressive and extremely destructive pathogen that causes black pod disease of cacao, significantly limiting yield in the world's leading cacao producing region in West and Central Africa. To effectively use genetic breeding to improve cacao resistance to black pod disease, the genetic diversity of both host and pathogen populations must be considered. We examined genetic diversity and population structure of P. megakarya using genomic data from 166 isolates collected from Cameroon, Nigeria, and Ghana. We used reads from genotyping by sequencing of 150 isolates and from published whole genome sequences of 15 isolates to call 2,644 high quality SNPs relative to the reference genome Pm1/GH34 from Ghana. Isolates could be assigned to one of two major clades. One clade contained isolates from Nigeria and Ghana and the other contained isolates collected in all three countries. The two major clades showed differing degrees of genetic variation among isolates and heterozygosity of SNPs. Genomic data will be integrated with isolate phenotypes determined using experimental inoculations of cacao pods to evaluate variation in genetic determinants of virulence in P. megakarya.