Morphology of some groups of organisms has been highly conserved over evolutionary time, resulting in genetically divergent taxa with relatively little morphological variation. Genetic studies on salamanders of the genus Plethodon have revealed a high level of morphologically cryptic diversity, and recent ecological and evolutionary studies have suggested that morphology may be informative for taxonomic purposes when combined with genetic data. We examined morphological variation in the Ouachita Mountain endemic salamanders P. fourchensis and P. ouachitae to test whether these sister species, and recently identified phylogeographic lineages within species as defined by genetic data, can be discriminated using morphology. We found that P. fourchensis and P. ouachitae differed significantly in morphology and could be classified correctly with greater than 90% accuracy. Individuals from a previously identified hybrid zone were morphologically intermediate to the two parental species. Phylogeographic lineages within each species (n  =  4 for P. fourchensis, n  =  7 for P. ouachitae) also exhibited significant morphological differences and were classified correctly in 57–72% of cases. Our results support genetic evidence that showed significant divergence between P. fourchensis and P. ouachitae and among the different lineages within each species. The high levels of diversity within P. fourchensis and P. ouachitae have important implications for conservation because these endemic species have small ranges and lineages are usually restricted to single mountains.