Abstract Mitochondrial DNA sequences of three individuals of the harbour porpoise (Phocoena phocoena) sampled in the Black Sea, Marmara Sea and Aegean Sea, revealed three polymorphic sites, resulting in three different haplotypes. None of the haplotypes obtained in this study clustered with those in the Atlantic populations, consistent with previous findings. The Black Sea and the Aegean haplotypes sequenced in this study had been previously detected from the Ukraine coast of the Black Sea, supporting the idea that harbour porpoises from the Black Sea dispersed into the northern Aegean through the Istanbul and Çanakkale Straits. The third sample from the Marmara Sea had the same unique haplotype as the one found in three individuals from the same sea in an earlier study. This structuring supports the possibility of an isolated population in the Marmara Sea. It should also be noted that this is the first genetic study of the harbour porpoise, inwhich a sample from the Turkish coast of the Northern Aegean Sea was studied.