Abstract. To find out if native and introduced European eel (Anguilla anguilla) populations differ from one another genetically, we used five microsatellite markers and compared naturally recruited and introduced European eel populations at four different locations. Samples of naturally recruited eels were taken from the Baltic Sea and the Curonian Lagoon, while introduced eels were sampled from Lakes Dringis and Siesartis. Results of the study do not support the hypothesis on panmixia in the European eel, since low but significant genetic differentiation (F ST = 0.0238, p = 0.0148) was found to exist among introduced eel groups. Significant genetic differentiation (F ST = 0.0228, p = 0.0281) among the Baltic Sea, the Curonian Lagoon, Lake Dringis and Lake Siesartis populations was ascertained too.