The New Zealand mudsnail Potamopyrgus antipodarum is one of most widespread invasive species worldwide. Two phenotypically diverse but genetically mostly uniform clones have been reported in Europe, typically occuring allopatrically. It has been suggested that salinity may determine distributions of the two lineages in Europe, but the hypothesis remains speculative. The snail has recently expanded its distribution area into Central European lakes, but the clonal affinity and ecological tolerances of the species have not yet been assessed. In this study, we use mitochondrial and nuclear genetic markers to explore the diversity of P. antipodarum in 19 locations in Lithuania, Poland, Ukraine and Finland. We first confirm congruence between the independently reported mitochondrial and nuclear lineages, now called multi-locus lineages T and Z. Both lineages were found in the studied area, and, in agreement with earlier studies, both showed extremely low genetic diversity. Only lineage T occured in freshwater ecosystems in Central Europe, whereas only lineage Z was found in brackish waters of the Black Sea basin. Both lineages occur in the Baltic Sea, although mostly allopatrically. It could be expected that the lineage T will expand its distribution area in the Central European freshwater ecosystems, but further studies are needed to understand the origins and occurrence of the lineage Z in the Baltic Sea and southern Ukraine.