Vibrio parahaemolyticua and Vobrio alginolyticus are phylogenetically closely-related species. They have common ecological niches, same cultural features and similar biochemical characteristics. The phenotype variability and taxonomy similarity of strains of these species impedes differentiation of Vibrio parahaemolyticua and Vobrio alginolyticus according biochemical characteristics. To obtain reliable results of diagnostic application of additional methods of differentiation and identification these two species of bacteria are needed. The study was organized to comparatively evaluate effectiveness of biochemical testing, polymerase chain reaction analysis and mass-spectrometry technique in differentiation of species of Vibrio parahaemolyticua and Vibrio alginolyticus. The study implemented analysis ofmethods of differentiation ofspecies of Vibrio parahaemolyticua and Vibrio alginolyticus using model of collection including atypical strains of these species. To substantiate species belonging of strains of Vibrio parahaemolyticua and Vobrio alginolyticus such techniques are to be additionally applied to biochemical methods of identification as polymerase chain reaction analysis with species-specific primers of genes of metalloproteinase (collagenase) vppC and vapC. The MALDI-TOFF method of mass-spectrometry can be used as additional effective method of identification and inter-species differentiation of species of Vibrio parahaemolyticua and Vibrio alginolyticus isolated from various sources.