Research carried out in the 84 expedition of RV "Professor Vodyanitsky" in the coastal waters of the Black and Azov sea, from 19 to 26 April 2016. 59 samples were taken at 20 stations within an upper 50-m layer of water. The average abundance of MMZP in the surface layer of the Black Sea waters was 14.8 ± 5.8 thousand ind. m^-3. The maximum number (up to 35 thousand ind. m^-3) were observed in the coastal waters of Kalamitsky and Karkinitsky bays, minimum (1-13 thousand ind. m^-3) – in the waters of south coast of Krimea. In the Azov Sea MMZP abundance was almost an order of magnitude higher and ranged from 52.4 to 198.6 thousand ind. m^-3 – on the surface, and from 39.0 to 89.0 thousand ind. m^-3 – in the bottom layer. Species composition of the MMZP in the Black Sea waters characterized by the predominance of crustacean fraction and copepods as it`s base foundations: respectively, 81.9 and 77.4% of the total abundance. In the Azov Sea were dominated meroplanktonic larvae of barnacles (over 65%); larvae of polychaetes, bivalve veliger and rotifers were abundant, also. The character of the vertical distribution depended on the predominant composition of micrometazooplankton: the mollusk veligers determined the abundance maxima in the middle and lower layers of the water column in the shallow-water zones; in deeper habitats, copepods predominated, which determined local maxima in different layers.