The subterranean aquatic snails may serve as a model of endemism and isolation vs. migration in subterranean habitats. The aim of the present paper is to verify the hypothesis that subterranean aquatic snails can migrate through diverse subterranean habitats, applying four molecular markers as well as a RAPD technique and shell morphometry. They were used to estimate the differences and gene flow between populations of the hydrobiid subterranean aquatic species Montenegrospeum bogici, collected in the Dinaric karst region. Three molecularly distinct taxonomic units were distinguished. The mOTU B was found at single locality, mOTU C at two, but the mOTU A at ten localities, scattered along 236 km distance, at two of them in sympatry with either mOTU B or C. Within mOTU A, the estimated levels of the gene flow were high. The pairwise measures of genetic differentiation were statistically significantly associated with geographic distances between the populations. In general, neither the infinite-island model of interpopulation differentiation, expected for isolated populations, nor the stepping-stone one, but rather the isolation-by-distance model explained the observed pattern. Our results suggest that interstitial habitats provide ways of migration for the stygobiont M. bogici, as has been already suggested for other subterranean gastropods.