Numerous mechanisms drive ecological speciation, including isolation by adaptation, barrier, distance, environment, hierarchy, and resistance. These promote genetic and phenotypic differentiation of local populations, formation of phylogeographic lineages, and ultimately, completed speciation via reinforcement. In contrast, it is possible that similar mechanisms might lead to lineage cohesion through stabilizing rather than diversifying ecomorphological selection and the long-term persistence of population structure within species. Processes that drive the formation and maintenance of geographic genetic diversity while facilitating high rates of migration and limiting phenotypic divergence may thereby result in population structure that is not accompanied by divergence towards reproductive isolation. We suggest that this framework can be applied more broadly to address the classic dilemma of “structure versus speciation” when evaluating phylogeographic diversity, unifying population genetics, species delimitation, and the underlying study of speciation. We demonstrate one such instance in the Seepage Salamander (Desmognathus aeneus) from the southeastern United States. Recent studies estimated up to 6.3% mitochondrial divergence and 4 phylogenomic lineages with broad admixture across geographic hybrid zones, which could potentially represent distinct species. However, while limited dispersal promotes substantial isolation by distance, extreme microhabitat specificity appears to yield stabilizing selection on ecologically mediated phenotypes. As a result, climatic cycles promote recurrent contact between lineages that are not adaptively differentiated and therefore experience repeated bouts of high migration and introgression through time. This leads to a unified, single species with deeply divergent phylogeographic lineages that nonetheless do not appear to represent incipient species.