The quagga mussel Dreissena rostriformis bugensis, native to the Dnieper and the northern Black Sea, has become a major invasive species in both the Volga River and the North American Great Lakes since the early 1990s. Findings in the Netherlands (2006) and Germany (2007) mark the start of its establishment in Western Europe. We investigated the current distribution, time of first arrival and population structure of D. rostriformis bugensis from the rivers Rhine, Main and in the Main-Danube canal in Germany. Two putative sources of the German populations were analysed by genetically comparing these populations to older invasive populations from North America and the southeast Danube. Dreissena rostriformis bugensis was abundant in the Main and in three Rhine harbours, but rare in the actual Rhine river and absent south of the Main-Danube canal. Mussels found in the Rhine harbours were significantly smaller than in the Main. Population genetic analyses found no sign of founder effects and minimal differentiation between German, North American and southeast Danube populations. The genetic data suggest that these invasive populations derive from a common and rapidly expanding source. Based on the non-continuous distribution and shell size differences of Rhine harbour and Main populations, our results indicate that expansion in Germany involved at least two independent settling events, one of which happened before 2005, and most likely was caused by jump dispersal.