63 Common Tern samples from Croatia and Slovenia were analysed with respect to their genetic diversity and differentiation. Samples originated from two freshwater populations (areas of the rivers Sava and Drava) and one coastal population (Sečovlje Salina). The molecular marker of choice was 709 bp long fragment of the mitochondrial control region, the fastest-evolving part of the mitochondrial genome. 21 haplotypes with 12 polymorphic sites were identified. Overall haplotype diversity was substantial and estimated at 0.8599, while the overall nucleotide diversity was low and estimated at 0.0025. Diversity indices were highest for the Drava population, followed by the Sava and the lowest for the Sečovlje population. Overall genetic structure was significantly low (Fst=0.0377) and attributed to the differences in haplotype frequencies between the populations. The high level of genetic diversity found in continental populations illustrates the importance of their habitats as reservoirs of genetic diversity and calls for their further protection and management.