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In this study mitochondrial DNA D-loop gene sequencing was used to investigate genetic structure of 11 Atlantic bonito Sarda sarda populations from the Black Sea, Marmara, Aegean, Mediterranean Seas and Adriatic Sea. The total sequence length, variable sites and parsimony informative sites were 868 bp, 12 bp and 7 bp from 222 individuals, respectively. The nucleotide frequencies were 32.55% A, 31.32% T, 14.44% C, and 21.68% G. The total number of haplotypes was 19, and the highest number of different haplotypes was observed in the nortestem Mediterranean (the Iskenderun Bay) sample, and the lowest was observed in the Bulgarian sample. Low genetic diversity was observed within populations, and the mean genetic diversity within populations and the mean genetic divergence between populations were 0.0009 and 0.0013, respectively. In the statistical analysis, S. sarda was divided into three genetically different populations (P<0.001); the Black and Marmara Sea populations comprise one genetic unit, and the Aegean and Mediterranean coast of Turkey populations constitute the genetically different second unit. The Adriatic Sea population from Croatian coast was also genetically different from these two units. The neighbor joining tree revealed three main phylogenetic nodes; in the first node, the Black Sea, Bosphorus and Marmara Sea samples were grouped close together. In the second main node; the Aegean and northeastern Mediterranean Seas samples were clustered close to each other, and the Adriatic Sea sample was far from these samples, but closer to the Aegean and northeastern Mediterranean samples than the Black Sea and Marmara Sea samples. [ABSTRACT FROM AUTHOR]