The study was targeted to apply mass spectrometry analysis for inter-specific differentiation of collection strains of representatives of genus vibrio and identification of comma bacilli extracted from samples of boat ballast waters. The samples consisted of 207 museum strains of cultures and 347 microorganisms from samples of boat ballast waters. The identification of microorganisms was implemented using MALDI-TOF mass spectrometers. The application of MALDI biotyping made it possible to detect inaccuracies in specific and generic characteristics of collection strains V. alginolyticus, V. parahaemolyticus, Shewanella, V. mimicus and to enhance characteristic and quality of collections of microorganisms. The effective application of MALDI to monitor boat ballast waters is demonstrated. This technique allows detecting of complete vibrio landscape of pathogenic and non pathogenic genus. The possibility to detect strains of comma bacillus and cholera agents is demonstrated. The mode of orientation on V. albensis at the stage of selection of suspicious colonies is proposed.

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