This paper presents the results of contamination level of sea bottom sediments and seawater in the water areas by the strait of the Black Sea and the Azov Sea by oil hydrocarbons and chloroform-extractable substances studies (spring, autumn 2016). Comparison of marine environment pollution levels with the results of previous studies (2007–2010) and sanitary norms is given. The quantitative characteristics of heterotrophic and oil-oxidizing microbiota in the designated areas are presented. It was determined that the concentration of oil hydrocarbons in the water surface layer in the water area by the strait of the Azov Sea did not exceed the current norm (0.05 mg·l-1). The single cases of the maximum permissible concentration exceeding were registered in the water area by the strait of the Black Sea (autumn 2016). In the surface layer of Azov Sea water, the number of heterotrophic bacteria ranged from 104 to 105 cells·ml-1, and the oil-oxidizing bacteria were isolated in single quantities. In the water area of the Black Sea region of the strait the number of heterotrophic bacteria was 106, the number of oil-oxidizing bacteria did not exceed 10 cells·ml-1. In comparison with the previous years’ data, there was an increase in quantitative indicators of chloroform-extractable substances and oil hydrocarbons in the sea bottom sediments. The overall level of pollution did not exceed the average values determined for the region. The number of heterotrophic bacteria in the sea bottom sediments varied in the Strait of Azov water area from 2,5·104 to 4,5·104 cells·g-1, while that of oil-oxidizing bacteria varied from 2,5·10 to 4,5·102 cells·g-1. In the sea bottom sediments of the Black Sea, the number of heterotrophic bacteria was 4,5·103 cells·g-1, the number of oil oxidizing bacteria was 10 cells·g-1.