Life-history characteristics are an important determinant of a species’ dispersal abilities. We predict that variation in life history can influence population-level genetic patterns. To test this prediction, we estimate population-level genetic structure for two sympatric species of stream-breeding salamander. The Cope's giant salamander (Dicamptodon copei) rarely metamorphoses into a terrestrial adult, thereby limiting overland dispersal and potentially gene flow. In contrast, the Pacific giant salamander (D. tenebrosus) commonly metamorphoses, which is expected to facilitate overland dispersal and gene flow. Three sets of analyses based on microsatellite data support these hypotheses, showing that D. tenebrosus displays minimal population-level genetic structuring and no pattern of isolation by distance, whereas D. copei displays a high degree of population-level genetic structure and significant isolation by distance. Specifically, nearly all pairwise FST values were significantly different from 0 between populations of D. copei, with fewer than half the pairwise FST values significant from 0 in D. tenebrosus. Additionally, Structure analyses indicated eight genetic clusters for D. copei but only one genetic cluster for D. tenebrosus. Finally, Mantel tests showed significant correlations between stream and overland distance with genetic distance for D. copei but no significant correlations of either landscape feature for D. tenebrosus at the scale of the study. These results provide a case study of the link between life-history variation and population genetic patterns while controlling for phylogeny and environmental variation.