The genetic characteristic of seriously threatened river lamprey Lampetra fluviatilis L. from Vistula river and Vistula lagoon (Poland) was described in the present paper. The study, based on the nine microsatellite markers, was conducted to determine the genetic diversity and population structure of river lamprey in Vistula river and Vistula lagoon in Poland. Observed heterozygosity ranged from 0.158 to 0.974 in lamprey from Vistula river, and 0.040 to 0.990 in lamprey from Vistula lagoon. The expected heterozygosity in river lamprey ranged 0.177–0.673 in specimens and 0.213–0.670 in population from Vistula lagoon. Eight loci appear to be diagnostic, due to occurrence of private alleles, for distinguishing the Vistula river and Vistula lagoon populations. The estimated effective population size (Ne) for the studied populations of river lamprey form Vistula river and Vistula lagoon equalled 72.4 (95% CI = 14.9–∞) and 25.8 (95% CI = 8.7–151.1), respectively. Constructed individual’s tree based on DAS genetic distances and the Principal Coordinates Analysis (PCoA) exhibited three main genetic groupings within studied fish group. The presented genetic characteristic of studied lamprey populations is important and necessary to develop and implement conservation actions of river lamprey in Poland
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