Aim: Habitat specialization can constrain patterns of dispersal and drive allopatric speciation in organisms with limited dispersal ability. Herein, we tested biogeographic patterns and dispersal in a salamander with surface-dwelling larvae and obligate cave-dwelling adults. Location: Ozark Plateau, eastern North America. Methods: A population-level phylogeny of grotto salamanders (Eurycea spelaea complex) was reconstructed using mitochondrial (mtDNA) and multi-locus nuclear DNA (nucDNA), primarily derived from anchored hybrid enrichment (AHE). We tested patterns of molecular variance among populations and associations between genetic distance and geographic features. Results: Divergence time estimates suggest rapid formation of three major lineages in the Middle Miocene. Contemporary gene flow among divergent lineages appears negligible, and mtDNA suggests that most populations are isolated. There is a significant association between phylogenetic distance and palaeodrainages, contemporary drainages and sub-plateaus of the Ozarks, as all features explain a proportion of genetic variation. However, the combined effects of palaeodrainages and sub-plateaus explain the greatest proportion of genetic variation. Main conclusions: The geological and hydrological history of the Ozark Plateau has influenced lineage diversification in the grotto salamander, leading to genetic isolation among populations. Limited gene flow and strong phylogeographic structure in this complex may result from the restriction of highly specialized adults to caves.