The results of the monitoring of ballast waters of commercial vessels and research on the ecosystem biodiversity of the Novorossiysk Port are reported. Data on structure of immigrant fauna, its abundance, survival and origin of species were obtained. It has been established that the risk of introduction of Mediterranean species into the Novorossiysk Bay is the most probable. The basic "risk groups" are copepods and polychaetes. It has been hypothesized, that ship ballast water can become a primary factor of the "mediterranization" of the copepod fauna (Copepoda) in the northeast of the Black Sea. During the period of research in the Novorossiysk Bay, 36 species of Mediterranean copepods were recorded. A massive number of the cyclopoid copepod Oithona brevicornis Giesbr., 1891, a new species for the Black Sea, was recorded in samples collected in the autumn of 2005 and 2006. The status of the invader was attributed to the polychaete of the Streblospio genus. The necessity of ship ballast water control in Russia and the development of methodology, methods, and regulations for the prevention of the intrusion of pathogenic and potentially dangerous organisms by marine traffic were corroborated.