This study provided a preliminary comparative analysis of meiobenthic assemblages in different habitats of the Snake Island Marine Protected Area (MPA). Meiobenthos was studied in three habitats: Exposed Black Sea upper infralittoral rock with Corallinales turf (MB142), Mytilid dominated exposed Black Sea upper infralittoral rock with foliose algae (no Fucales) (MB143) and Black Sea infralittoral sand and muddy sand without macroalgae (MB542). A total of 10 higher meiobenthos taxa were recorded in the different habitats: 5 permanent groups (Platyhelminthes, Nematoda, Harpacticoida (Copepoda), Ostracoda, Halacaridae) and 5 temporary groups (Oligochaeta, Polychaeta, Bivalvia, Gastropoda, Cyrripedia). The preliminary study of meiobenthos in the habitats of the Snake Island MPA showed that habitat MB143 was more favourable for meiobenthos, with the highest mean density and biomass (190655 ± 23004 ind.-m-2 and 3170.90 ± 412.15 mg-m-2, respectively). The comparative nMDS and cluster analyses based on the density of meiobenthos taxa in the Snake Island MPA showed that the meiofauna of both MB142 and MB143 differed significantly from the MB542 habitat, with Bivalvia and Ostracoda making the largest percentage contribution to these differences. The meiobenthos assemblages in the different habitats of the Snake Island MPA were similar to the other regions of the Black Sea with some unique features (e.g. relatively lower total meiobenthos density, high percentage of ostracodes on the algal substrate, etc.). Further studies on the characteristics of meiobenthos taxa assemblages in other Black Sea MPAs could lead to the estimation of meiobenthos assemblage patterns and their possible use in biomonitoring.