Potato has two wild relatives native to the USA, Solanum jamesii (jam) and S. fendleri (fen). Core collections are a useful tool for genebanks, identifying a ranked minimum number of samples that together encompass most of the total genetic diversity. With diversity measured as presence of AFLP bands, we made core collections for each species such that >90 % of diversity was captured in a minimum of populations. For fen, bulks containing about 25 % of populations accomplished that standard. For jam, a single “mega-population” at Mesa Verde, CO, consisting of many thousands of plants, was found to encompass 82 % of the AFLP bands detected in all samples across the entire USA range, and adding three more populations captured a total of >90 %. Core members for both jam and fen with the most diversity originated from the northern part of the range. That suggests that these areas merit more collecting. If resources for germplasm preservation and evaluation are limited, samples in the core collections should take priority.