Blue-spotted salamanders (Ambystoma laterale) are a widespread and relatively common species throughout northeastern North America. The distribution of this species is marked by a pair of peripherally isolated populations at the southwestern boundary of its range in Iowa, a state where these salamanders are endangered. Because small peripatric populations suffer greater risks of extinction, the genetic state of the isolates was compared to that of a reference population that appears to be in geographic contiguity with the primary distribution of the species. Five polymorphic microsatellite loci were used to examine population genetic structure. Whereas allelic richness exhibited by each locus was qualitatively similar across study populations, genetic data indicate that the scaled effective population sizes of the peripheral isolates were demonstrably smaller compared to that of the reference population. One of the Iowa isolates shows evidence of a recent bottleneck and of substantial inbreeding; this population may therefore be subject to a particularly heightened risk of extirpation.