Genetic diversity and phylogeography was surveyed for the western Palaearctic water strider (Heteroptera, Gerridae) Aquarius najas (DeGeer) based on almost 780 bp of DNA sequence data from the mitochondrial gene encoding cytochrome oxidase c subunit I from 62 specimens sampled throughout its distribution area, and including the two related species A. cinereus (Puton) (6 specimens) and A. ventralis (Fieber) (3 specimens). 34 unique haplotypes were found for A. najas (55%), 5 for A. cinereus (83%), and 3 for A. ventralis (100%). A strict consensus tree obtained after a maximum parsimony analysis of the unique haplotypes was well resolved, and showed that while monophyly of A. ventralis was strongly supported, A. najas and A. cinereus were not reciprocally monophyletic in their mtDNA, since two clades from North Africa include a mixture of both species, and one specimen of A. cinereus from Sicily could not be assigned to any clade. All haplotypes were geographically well structured, and only one A. najas haplotype was widely distributed. This haplotype belongs to a clade with very little sequence divergence, which is distributed throughout Central and northern Europe, but includes also populations from northern Italy and northern Greece, thus indicating one or two possible refuges during the Pleistocene glaciations. Specimens from the Iberian Peninsula and Mallorca comprised a sistergroup to this clade, and show that the Iberian refugium did not contribute to the fauna of other parts of the European continent. Around the Mediterranean the sequence divergences for A. najas were much higher, especially in the Balkans, and on the islands Crete and Corsica. Whether the occurrence of these highly distinct lineages around the Mediterranean is due to extinction - or insufficient sampling - of intermediate haplotypes, or whether it indicates presence of unrecognized sibling species of A. najas and A. cinereus clearly needs further investigation.