The first research of the ballast waters of commercial vessels in Novorossiysk and Vladivostok ports are submitted. The data on structure of flora and fauna, their abundance, viability, and origin of species are received. In zooplankton of the ballast waters from Novorossiysk port, it was identified 31 species of holoplankton, 15 species of meroplankton. The average density of zooplankton varied from 1.3 up to 60∙103 ind/m3 . It has been established, that a vector of the greatest risk is the Mediterranean basin, from which 62% of water ballast enters. In the port of Vladivostok in ballast waters of vessels of the RussianJapanese and Russian-Chinese lines 45 species of microalgae, 24 species of a zooplankton, 22 species of a meroplankton, 10 taxa of meiofauna were revealed, 24 species microscopic filamentous fungi were identified, in the culture of two tests it was outlined 28 morphology distinguished strains of bacteria. The basic «groups of risk» of bioinvasions in the investigated ports were revealed. The need of the control of the ships’ ballast water in Russia, development of methodology, methods and laws for prevention of carrying of pathogenic and potentially dangerous organisms by a water transport is confirmed.