The genetic structure of two native Silurus aristotelis (one of Europe's oldest surviving freshwater fish species) populations was investigated using eight microsatellite loci. Average values of population heterozygosity were very high, even approaching values reported for marine fishes, possibly due to stable population sizes and the prolonged undisturbed conditions prevailing in the lakes that represent the native distribution of S. aristotelis. The success of an attempt to introduce the species into a new environment was also evaluated. No loss of genetic variability in the introduced population was detected. Additionally, assignment tests and trees based on genetic distances among individuals indicated the low differentiation of the translocated population from its donor population, and, differentiated the two autochthonous populations successfully. Comparisons with previous allozyme and mitochondrial RFLP studies were also made and showed that results on relative levels of genetic variability among populations were in good agreement among all methods. However, microsatellite analysis exhibited higher power of statistical tests for differentiation among population samples compared to allozymes.