Our previous study examining the effects of agrichemicals on the reproductive capacity of potato species revealed that the pesticide carbofuran negatively influenced flowering duration and pollen viability. These changes could limit reproductive ability non-randomly, modify allelic frequencies, and cause genetic drift. This study utilized Simple Sequence Repeat (SSR) markers to examine that possibility by assessing the genetic structure of progenies derived from potato populations exposed to two levels of carbofuran. A total of eight populations of five potato species (acl, buk, hcr, med and rap) were evaluated. An untreated, uncontaminated population was included as control for comparison. The results revealed that most of the 116 SSR allele frequencies assessed did not differ significantly between control and progenies of pesticide-contaminated parents. A few markers showed a significant frequency shift in some species, specifically buk and med. However, this study reveals that although the pesticide reduces reproduction in wild potato species populations, changes in population genetics are minor and do not significantly threaten diversity. © 2012 Potato Association of America.