Blue crab, Callinectes sapidus (Rathbun, 1896), is a commercially important crab species native to the Western Atlantic Ocean. Callinectes sapidus has invaded the Mediterranean Sea in 1930s and spread rapidly. It has become widely distributed and has been moving through adjacent basins including the Black Sea. In this study, mitochondrial 16S rRNA and COI sequences were generated for individuals captured from the Black Sea for the genetic characterization of the population for the first time. Additionally, available sequences of C. sapidus from their native and introduced populations were included in the analysis to evaluate phylogenetic affinities and the most probable origin of the population in the Black Sea. The Black Sea specimens were clustered with the sequences from the Northwest Atlantic Ocean on the basis of 16S rRNA sequence analysis and with those from the Northwest Atlantic Ocean and the Levantine Sea on the basis of COI sequence analysis. The Caribbean Sea and the Southwest Atlantic Ocean sequences were clustered together. Notable genetic divergence was observed between the populations of the Black Sea and the Levantine Sea. The present C. sapidus population in the Black Sea is most probably a result of the migration from the Aegean Sea (Saros Bay), where C. sapidus has established a stable, reproductively successful population. Patterns of the haplotype diversity and maximum likelihood trees indicate that the invasive population of C. sapidus in the Black Sea possibly originated from the Northwest Atlantic Ocean. Genetic divergence between populations of the Black Sea and the Levantine Sea were attributed to the limited sample size from the Black Sea.