Samples of tissues of the Common Tern (Sterna hirundo) breeding in Lithuania were collected in the colonies distributed in the basins of the River Nemunas and the River Dauguva located near Kalviai, Kietaviškės, the Nemunas delta, Lazdijai, Kretuonas, Zarasai and Ignalina. By means of 11 primer pairs designed for the analysis of microsatellite loci of taxonomically close bird species, allele frequencies at 11 polymorphic loci of the Common Tern were established. The heterozygosity ranged from 0.1809 to 0.4029 in separate colonies. No significant differences in the genetic variability of the colonies under study have been detected. However, a lower genetic variability was established for the Nemunas delta colony, which reflects a greater effect of natural selection. A high genetic differentiation was calculated for the entire population (R_ST = 0.1545). Deviation from the Hardy–Weinberg equilibrium as a deficit of heterozygosity was detected in six out of the seven colonies investigated. It might be caused by a high level of inbreeding and a genetic drift. The Common Tern subpopulations breeding in the basins of the River Nemunas and the River Dauguva are genetically differentiated and form separate clades in the dendrogram obtained using the UPGMA algorithm. The obtained data allow a conclusion that the differences in the genetic structure of the Common Tern colonies are influenced by the geographic distribution of large rivers.

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