The replacement of native species by invasive species is one of the most critical threats to the biodiversity of aquatic systems today. However, little is known about potential effects of species invasions on the genetic diversity of indigenous species in cases where the latter coexist with the invader. Here we present an example of the indigenous amphipod Gammarus roeselii, which has been partly replaced by the invasive Dikerogammarus villosus in Lake Constance (C-Europe) and now mostly exists in small, isolated populations. We compared the genetic diversity, population structure, indicators for bottlenecks and migrations rates of G. roeselii before and after the invasion event from samples collected between 1999 and 2013. We expected a genetic impoverishment in the reduced and segregated populations of G. roeselii. However, no genetic measure on G. roeselii differed temporally or spatially over the investigated period, which indicates that D. villosus has not yet had an impact on G. roeselii at the genetic scale. Hence, even though a decline in population size of G. roeselii was found in Lake Constance, our results on the genetic scale contribute to recent findings that the overall impact of D. villosus on native species is not as strong as often discussed.