Water scorpions belonging to the genus Nepa are predatory freshwater aquatic insects of the order Hemiptera. There are currently five accepted species, with a Holarctic distribution: N. cinerea (Eurasia and Northern Africa), N. sardiniensis (Sardinia and Corsica), N. anophthalma (endemic to Movile Cave, Romania), N. apiculata (North America) and N. hoffmanni (Eastern Asia). Mitochondrial and nuclear genetic markers indicate a correlation between genetic diversity and geographic distribution. Analyses also reveal a cryptic diversity in the Western Mediterranean basin, with specimens of the cinerea clade being assigned to the sardiniensis clade. The cave-adapted N. anophthalma is genetically closest to N. cinerea, suggesting surface populations of N. cinerea as possible ancestors. N. cinerea samples from three cave systems in Italy indicate various degrees of gene flow between surface and subterranean populations and an instance of a possible incipient speciation event. Despite the overlap in distribution range in mainland Eastern Asia between N. cinerea and N. hoffmanni, there is a high genetic distance between the two species. A similar value of genetic distance is found between N. cinerea and N. apiculata, but also between N. hoffmanni and N. apiculata, suggesting the assignment of N. hoffmanni and N. apiculata to different genera. The single species currently considered as stygobiotic, N. anophthalma, deserves more research to understand the timing of colonization of Movile groundwater by its surface ancestors.