A wide range of issues, related to the non-native species in the Sea of Azov, is being considered including main features of the physical geography, hydrology, and hydrochemistry, origins and composition of the flora and fauna, non-native biota composition, Mnemiopsis leidyi population and its effect on the ecosystem, and Beroe ovata and its contribution to the ecosystem recovery. Special attention is paid to environment deterioration in the Sea of Azov due to both natural (water warming due to the climate change) and anthropogenic interference (regulation of the rivers’ runoff and water withdrawal, industrial construction, irrigation systems, reservoirs construction, pollution etc.) and its effect upon the biota and fish stocks. One of the most disastrous consequences of massive freshwater runoff decrease was the salinization of the sea, which, in turn, facilitated migration of marine species of the Mediterranean or Atlantic origin from the Black Sea. It is noted that the changes in salinity in the Sea of Azov occurred in the form of pronounced phases of salinization/desalination.