Geographic analysis was carried out on a small number of morphometric characters and on the occurrence of integumental organs, i.e., supernumerary pores, on the ventral side of urosome segments 2 and 3 in adult females of Calanus helgolandicus s.l. Morphometry indicated the existence of two distinctive populations, one in the Black Sea, the other in the Mediterranean Sea and Atlantic Ocean. Significant differences in the frequency of supernumerary pores, however, indicated a Black Sea population, an east Mediterranean population, and a west Mediterranean-Atlantic population. Limited hydrographic exchange between the Aegean and Black Seas together with directional selection of the Black sea population adjusting to the unusual properties of its environment appears to have shifted the equilibrium of this gene pool to a position substantially different from that of the Mediterranean. It is argued that the usually low frequency of supernumerary pores characterizing the east Mediterranean population is a consequence of episodes of disadvantageous cross-breeding with Black Sea stocks which induced reinforcement of a pre-zygotic reproductive barrier. Gene flow between the east and west Mediterranean populations maintains homogeneity in morphometry, and the intermediate frequency of supernumerary pores in the west Mediterranean population suggests interbreeding with both the east Mediterranean and the Atlantic populations. Based on the evidence of reproductive incompatibility, the Black Sea population is recognized as a distinct species, namely, Calanus ponticus, and separate from C. heloglandicus which is restricted to the Atlantic and Mediterranean populations. Time constraints based on the geological history of the Black Sea require that this cladogenesis evolved during the 7,000 years of less before the present.