We examined the genetic population structure of Long-Toed Salamanders (Ambystoma macrodactylum) from the Bitterroot Mountains of Idaho and Montana to better understand their evolutionary history and genetic population structure. Populations show high levels of within-population genetic variation at six polymorphic allozyme loci (H̄_s = 0.09 for all 18 loci examined; range 0.04–0.14). There is very little divergence among populations within basins, suggesting panmixia within basins. In contrast, genetic differentiation among all populations is high (G_st = 0.30). We used computer simulations to examine population structures that could have led to the observed distribution of genetic variation, assuming selective neutrality of the allozymes. To test the assumption of selective neutrality of the markers used in this study, we compared the observed divergence among the allozymes to that expected from simulations of independently segregating and selectively neutral markers. The observed genetic divergence among populations is compatible with that expected for neutral genetic markers sampled from panmictic populations within basins that exchange less than one migrant among basins each generation.