1141 bp mtDNA fragment containing cytochrome b sequence was analyzed. Samples from the Caspian (53 individuals – marine, 57 – Volga, 6 – Kura and Arax), Baltic (36 – Lake Chudskoye), Azov (9 – Don), Aral (5 – Syr Darya), Aegean (31 – Kardzhali, Pyasachnik, Zhrebchevo) basins were analyzed. All identified haplotypes belonged to haplogroup A. Haplotype A (Slucb2) dominated in all samples except the Aegean ones. Haplotype A1 (differing by one substitution from A), distributed in water bodies of central Europe, was found only in Lake Chudskoye. The less common A2 (Slucb1) differing by 3 substitutions from haplotype A (Slucb2) occurred in most of the Ponto-Caspian samples. In addition, new haplotypes of A haplotype group were described. They differ by single substitutions from the main A and A2 haplotypes: three new haplotypes were found in Caspian Sea samples, one- in the Syr Darya River sample. Another previously undescribed haplotype was found in one individual from the Don and in all studied individuals from the Aegean basin (Bulgaria). This haplotype is transitional between haplogroups A and B. Thus, the absence of the haplotypes dominating in other parts of the range makes the pike-perch from the Aegean water bodies genetically unique.