Amphipods are keystone species in many freshwater ecosystems. Understanding their distribution and diversity is crucial to ensure and preserve freshwater ecosystem functioning, particularly in the northern hemisphere. For the European Alps information on amphipods has been relatively limited until recently. We describe a new, widely distributed amphipod species, Gammarus alpinus sp. nov., found across the Alps and analyse its distribution, biogeography as well as genetic and morphological differentiation. Until now, this species has been reported as Gammarus lacustris. Based on genetic and morphometric measurements, we show that G. alpinus is highly divergent from G. lacustris. The latter has a circumpolar distribution, but may be absent from the Alps. The observed occurrence pattern of G. alpinus might be explained by a Pliocene range expansion and vicariance due to climate warming following the Quaternary glaciation. Historical drainage divides suggest a single recolonization route from a distinct southern refugium. While G. lacustris is widely distributed and not endangered at a global scale, G. alpinus is endemic to the Alps and its habitat is negatively affected by eutrophication, non-native species and possibly climate change.