Two morphologically similar lionfish species Pterois miles and P. volitans (Scorpaenidae), reported in Turkish marine waters, were assess using partial mitochondrial cytochrome c oxidase I (COI) gene. As a result of sequence alignment, 609 bp of COI region were examined and it was contained 81 bp variable and 528 conservative sites of which 47 bp parsimony informative sites. Mean genetic diversity and genetic divergence between species was 0.009481 and 0.047660, respectively. 16 different haplotypes were detected in total 18 sequences, and there were no shared haplotypes between the two lionfish species. According to neighbor joining and maximum parsimony trees, P. miles and P. volitans were clustered in different clades.