Free living amoebae (FLA) are ubiquitous and found in many types of environments including soil, freshwater, air and marine environments. They feed on various microorganisms, and can play a key central role in the food web and its dynamic. We described previously that FLA belonging to the Vannella genus from the oyster farming area of the Thau lagoon in France could establish stable interactions with Vibrionaceae and could play a role in the selection of some virulence factors and potentially affect pathogen dynamics. To investigate further the ecological interactions between FLA populations and Vibrionaceae in Mediterranean coastal waters, we conducted a monthly sampling for one year in three contrasted sites. Free-living amoebae populations were isolated by culturing water and sediment samples on different bacterial lawns including E. coli SBS363 or V . tasmaniensis LGP32, V . crassostreae J2-9 and V . harveyi A01. Amoebozoa diversity was analyzed using v4-18S barcoding and revealed distinct communities of Amoebozoa between the sediment and the water column, with Vannellidae significantly enriched in the water column whereas Paramoebidae were significantly enriched in the sediments. Selection of grazers on different bacterial lawns revealed that V . tasmaniensis LGP32 inhibited the growth of most Vannellidae whereas V . crassostreae J2-9 inhibited the growth of a large part of Paramoebidae. These differences were further confirmed in functional grazing assays using isolates belonging to each Amoebozoa taxonomic group. Altogether, our results highlight that Amoebozoa diversity in marine waters and population dynamics still need to be studied in a more comprehensive manner and the role of these diversified grazers in shaping vibrio communities is complex and still poorly characterized in the environment.