The aim of our study was to provide a first overview of the population genetic structure of the invasive Chinese sleeper, Perccottus glenii, (Actinopterygii: Odontobutidae) in European water bodies. This species originates from inland waters of north-eastern China, northern North Korea and the Russian Far East. The 1172 bp long portion of the cytochrome b gene was sequenced from Chinese sleeper specimens collected from a variety of water bodies in Belarus, Bulgaria, Hungary, Germany, Latvia, Lithuania, Poland, Russia (European part) and Ukraine. Our study revealed that the invasive Chinese sleeper in Europe consists of at least three distinct haplogroups that may represent independent introduction events from different parts of its native area; i.e. three founding populations: (1) Baltic haplogroup that may originate either from fish introduced inadvertent from Russia or from some unidentified source (release by aquarists). So far, this haplogroup has been found only in the Daugava basin in Latvia. (2) East-European haplogroup that may originate from an unintentional introduction to the Volga basin in Russia and has expanded westward. So far, this group was recorded in the Volga, Upper Dnieper and Neman drainages in Belarus, Lithuania, and Russia. (3) Carpathian haplogroup, that originated from individuals unintentionally introduced with Asian cyprinid fishes to Lviv region in Ukraine and are now widely distributed in Central Europe.