Ethological reproductive isolation and genetic divergence across 26 protein loci were measured among populations of the salamander Desmognathus ochrophaeus in the southern Appalachian Mountains. Levels of ethological isolation varied from none to complete and were statistically significant for all but two pairings between populations inhabiting different mountain ranges. When geographic and genetic distances were treated as independent variables in multiple correlation analyses, they accounted for about half the variance in levels of ethological isolation. When genetic distance is held constant, the remaining relationship between ethological isolation and geographic distance is still statistically significant. When geographic distance is held constant, the remaining relationship between genetic distance and levels of ethological isolation is nonsignificant, as is the relationship between geographic distance and genetic distance when ethological isolation is held constant. Ethological isolation and genetic divergence evidently both reflect the gradual divergence of allopatric populations, but genetic distance is a poor predictor of ethological isolation in these salamanders.