A comparison between twelve gobiid species from the Black Sea coast, coastal lakes and rivers was carried out on the basis of genetic-biochemical analysis (starch gel electrophoresis and isoelectric focusing on thin and ultrathin gel plates). Eleven enzymes and one non-enzyme protein system on starch gel (encoded by 29 loci) and general muscle protein loci on IEF (encoded by 22 loci) were studied. A single registered case of interspecies hybridization between Neogobius (Apollonia) fluviatilis and Neogobius syrman in Mandra Lake is proof that hybridization among this group happens only accidentally because of the fact that gobies exhibit parental care toward the eggs. First data for genetic-biochemical characteristics of Knipowitschia longecaudata are reported. Genetic distances (D-Nei = 1.10) between Knipowitschia caucasica and K longecaudata showed species specific differences. Genetical markers found for both species can be used for fast and precise identification. The received data are useful for the assessment of population status, taking into consideration that both species are threatened with extinction. Polymorphism on EST-3*, EST-4*, LDH-B*, sMEP-1*, sMEP-2* and MDH-1* loci can be used for the assessment of population infrastructure of Neogobius (Apollonia) melanostomus, Gobius niger, Pomatoschistus marmoratus and K caucasica. The mobility of electrophoretical patterns of LDH*B locus were used as markers in determining the genus status of Gobius ophiocephalus. The hypothesis that N. fluviatilis and N. melanostomus belong to the subgenus Apollonia was confirmed using LDH-B* locus as a genetic-biochemical marker. The four new enzymic systems (ADH, GPI, GLUDH and G3PDH) applied in the gobiid taxonomy gave species-specific spectra and can be used successfully as protein biomarkers. Their significance for the precise identification of species and populations, especially of those with minor morphological differences, as well as for the study of invasion pathways can increase in the future. Taxonomic investigations based on genetic analyses will contribute to biodiversity protection and conservation, to restoration and conservation of vulnerable gobiid populations and to sustainable fishery.