In this study randomly amplified polymorphic DNA (RAPD) fingerprinting is proposed for species identification of Gammarus, based on the electrophoretic position of amplified DNA bands. Three common marine amphipods of European estuaries—G. chevreuxi, G. insensibilis and G. locusta—were profiled using ten RAPD primers, accompanied by a careful morphological identification. Nine of these primers produced a very distinct species-specific RAPD profile, allowing unambiguous differentiation of amphipod species assayed. The RAPD fingerprints were here characterized by 8–12 amplicons for each primer. Each amplicon was visualized as a band of known molecular length, with characteristic band thickness and density. A total of 78 diagnostic bands, based on the most robust and evident amplicons found for each primer and species, are proposed for identification of the Gammarus species analysed. These results allowed us to identify an unknown amphipod species from a previous study as G. insensibilis, only based on the RAPD fingerprint. One primer was sufficient for this identification. A taxonomic identification system integrating molecular and morphological tools is proposed for Gammarus.