On the Aliulik Peninsula (AP) of Kodiak Island, Alaska, 70% of male Sitka black-tailed deer (SBTD; Odocoileus hemionus sitkensis) are bilaterally cryptorchid (both testes fail to descend; male is sterile). Both genetic and environmental factors have been proposed as possible causes of this problem. We investigated the possibility that population genetic processes (isolation, inbreeding and genetic drift) have contributed to an increased frequency of cryptorchidism in this population. Overall, SBTD on major islands throughout Alaska have unusually low levels of genetic diversity, though we identified a likely glacial refugium on Prince of Wales Island in the Alexander Archipelago. Within the Kodiak Archipelago, deer on the AP did not exhibit the patterns of genetic isolation, inbreeding and drift that would be expected if cryptorchidism in this population was the result of a founder mutation(s). Instead, our data favor exposure to environmental contaminants as a likely alternative mechanism causing high prevalence of cryptorchidism on the AP.