We lack critical information for oceanic archipelagos worldwide related to the origin and status of insular faunas. In southwestern Alaska, in particular, a need exists to tease apart whether specific insular populations are naturally occurring or are the result of exotic introductions by humans. We analyzed variation in mitochondrial sequences of the cytochrome-b gene and 8 nuclear microsatellite loci across 215 individuals representing 17 populations (12 insular) to refine our understanding of the history of the previously identified Southwest clade of arctic ground squirrels (Spermophilus parryii). We found significant geographic structure that suggests long-term isolation and diversification (Ushugat Island and Cold Bay), but we also documented closely related populations that are likely the result of human-mediated introductions. The latter instances (Kavalga and Unalaska islands) corroborate reports from early Alaska explorers.