Calanus helgolandicus is a widespread epipelagic copepod species whose geographical range extends from the temperate Atlantic Ocean to the northern Mediterranean Sea. Calanus euxinus, recently designated as a distinct species though closely related to C. helgolandicus, occurs in the Black Sea. Very subtle morphological differences distinguish the two species. Pseudocalanus elongatus has a similar geographic range including North Atlantic Ocean, Mediterranean Sea and the Black Sea. In this study, population genetic variation of C helgolandicus, C euxinus and P. elongatus was investigated using DNA sequence variation of 540 base pair (Calanus spp.) and 575 base pair (P. elongatus) regions of mitochondrial cytochrome oxidase I (mtCOI) gene. C helgolandicus was collected from the English Channel, the Adriatic Sea, and C euxinus was collected from various regions of the Black Sea. P. elongatus was collected from the English Channel and the Black Sea.