Knowing how genetic diversity is partitioned among and within wild potato species populations is important for efficient sampling for collection, preservation and evaluation. We sought to evaluate the effectiveness of SNPs for assessing germplasm by using the exact set of four model species previously evaluated by RAPDs. To avoid large numbers of SNP samples, population bulks of 25 plants were used, and original RAPD data was adjusted to match SNP genotype data. It was noted that especially for SNPs, it was necessary to examine only loci polymorphic within species to get a realistic view of genetic partitioning within species. This resulted in only a few hundred useful loci for some species. When considering among-population versus within-population partitioning of diversity, both SNPs and RAPDs distinguished the species as expected according to their known breeding system. Primitive wild species were confirmed as very heterogeneous within their populations. Both SNP and RAPD markers can be used to help breeders and genebank managers understand patterns and use in potato germplasm diversity.