ABSTRACT. – In this study the genealogical relationships and distribution of molecular variation of the mysid Neomysis integer was examined throughout most of its geographical range, in order to interpret phylogeographic patterns. N. integer (Leach, 1814) is one of the most common mysids (Crustacea, Mysida) along the coasts of Europe. It is a hyperbenthic species that typically dominates the brackish part of estuaries and occurs along the northeastern Atlantic from the Baltic Sea to Morocco. Nine samples, comprising 45 individuals, were collected across the species’ range of distribution, and sequenced using a segment of 390 base pairs of the mitochondrial cytochrome b gene (cyt b). A clear geographic structuring was found with one common haplotype occurring in most samples, while two samples (the Guadalquivir and Gironde estuary) consist solely of unique variants. At the southern distribution range a remarkable genetic break was observed between the Guadalquivir population and all other samples. These findings are discussed in the perspective of the presence of glacial refugia and postglacial recolonisation routes of low-dispersal organisms along the northeastern Atlantic coasts.