This paper presents a study on the microbial status of different fish species and their habitats in the Bulgarian Black Sea area. The samples were collected in the period of January 2021 until March 2021. The fish species we used in this study were Black Sea turbot (Scophthalmus maximus), round goby (Neogobius melanostomus), shore rockling (Gaidropsarus mediterraneus) and European anchovy (Engraulis encrasicolus). The BIOLOG system was used for microbiological determination. From the different fish species, different species of microorganisms were isolated (using selective nutrient media). From the torbut, we isolated species Enterococcus villorum with 24 × 103 cells in 1 ml, Moraxella nonliquefaciens with 70 × 103 cells in 1 ml and Pseudomonas synxantha with 123 × 103 cells. Pseudomonas putida was isolated from the round goby with 20 × 103 cells in 1 ml. The species Streptococcus entericus with 123 × 103 cells in 1 ml was isolated from the shore rockling. Pseudomonas fulva with 60 × 103 cells in 1 ml was isolated from the European anchovy. A total of 223 × 103 cells in 1 ml of Pseudomonas agarici were isolated from Trachinus draco. Pseudomonas tolaasii with 145 × 103 cells in 1 ml were isolated from Merlangius merlangus. A different species of bacteria of the genus Pseudomonas was found for each of the investigated species of Black Sea fish. Apparently, the species Pseudomonas is characteristic of marine Teleostei and is important for the life and metabolism of these vertebrates. These microorganisms probably are resident species and developed not as result of pollution or environmental change.