Nucleotide sequence divergence in mitochondrial cytochrome c oxidase subunit I (COI) gene was used to determine genetic variation of blue crab (Callinectes sapidus) populations found along Mediterranean coast of Turkey. 143 individuals from 8 distinct populations (Akyatan, Fethiye, Beymelek, Gulluk, Iskenderun, Koycegiz, Mersin and Tasucu) along Mediterranean coast were investigated by means of nucleotide composition and nucleotide pair frequency. Genetic divergence was estimated using DNA sequence variations, under Tamura 3-parameter model. Considering 143 individuals sequenced, 42 (6.41%) variable sites and an average vari-ation of 1.9% were found in 655 base pair long fragment. Highest genetic divergence was found between Akyatan-Gulluk populations; with a genetic distance rate of 2.5% and an aver-age value of R was estimated as 3.59 for all the populations. Phylogenetic tree was constructed using unweighted pair-group method of arithmetic average (UPGMA) method. When we eval-uated the phylogenetic tree with the sum of branch length of 0.07232, results point out a ge-netic structuring between blue crab populations correlated with the geographic distance.