By using simple sequence repeats (SSR) and random amplification of polymorphic DNA (RAPD) markers, the genetic variability of three Salmo trutta L. populations from three rivers, the Wieprza, the Rega and the Parseta, was determined. The investigated populations showed a high level of genetic variability. Microsatellites showed that observed heterozygosity (Ho) was higher than the expected heterozygosity (He), with most heterozygotes found in the population from the Parseta river and the fewest in the Wieprza population. The F(IS) coefficient in all investigated populations of the sea trout indicate a high excess of heterozygotes. The highest genetic differentiation was observed between the sea trout from the Rega river and those from the Wieprza (0.366). The obtained results based on microsatellite and RAPD analysis showed that the investigated populations formed two groups. The first group consisted of the sea trout populations from the Wieprza and the Parseta rives, while the second group was formed solely by the Rega river population.