The goal of germplasm conservation in genebanks is to maximize genetic variation. Collecting explorations would be more efficient if factors that predict areas and habitats associated with greater genetic differences and diversity could be identified. Therefore, the objective of this research was to investigate whether ecogeographical variables have significant associations with patterns of genetic variation in wild potato populations. This study examined 96 wild potato populations collected from the southwestern USA. These were 43 populations of Solanum fendleri (2n = 4× = 48) and 53 populations of S. jamesii (2n = 2× = 24). These species represent two of the most predominant breeding systems found among Solanum species: Tetraploid inbreeders and diploid outcrossers, respectively. Random amplified polymorphic DNA (RAPD) markers were used to assess populations in two ways: Determination of simple genetic difference between pairs of populations, and genetic diversity of a population based on the frequency of that population's RAPD markers in the whole set. Results from 2282 comparisons indicated that patterns of genetic differences were not associated with any differences in ecogeographical structure assessed. Remarkably, even geographical separation of populations, a parameter usually considered important when collecting germplasm, did not predict genetic differences very well. Latitude, longitude, and heat-related factors significantly predicted genetic diversity in S. fendleri but not in S. jamesii. This experiment revealed few associations between ecogeographic parameters and genetic variation in the wild. It follows, therefore, that one should collect many populations and incorporate a manageable subset into the genebank on the basis of empirical measurements of genetic diversity.