The Niphargus kochianus group is one of the most westerly and northerly components of the genus Niphargus. All taxa within the group were delimited by morphological characters. However, recent research suggests that morphology alone is inadequate in determining species boundaries in troglobiotic organisms. We used two molecular markers to examine nucleotide diversity in two members of the N. kochianus group, and included other taxa from Genbank. The results indicate that N. kochianus kochianus and N. kochianus irlandicus are very divergent taxa, which have had no common ancestor since the Miocene. Since it is very difficult to reconcile this magnitude of divergence with a recent derivation of irlandicus from kochianus, and there has been a sea water barrier between Great Britain and Ireland for a long period we propose that irlandicus has been resident in Ireland throughout the Pleistocene glacial cycles. Survival in sub-glacial refugia is supported by the presence of species below ice in Iceland and Canada, by the favourable biotic and abiotic conditions under glaciers, and by the physiology of species in the genus. The taxon irlandicus should therefore be considered a separate species Niphargus irlandicus Schellenberg, 1932.