Micropaleontological studies of the Black Sea, including ostracod records, have suggested that early Holocene salinity values were between ~5 and 10 practical salinity units (psu), contrasting with present values of 18–22 psu. However, more precise paleoenvironmental reconstructions based on ostracod assemblages require additional information related to their modern ecological affinities. This study uses modern species information collected from samples with living fauna to interpret the fossil Holocene assemblages of two sediment cores, Ak-2575 and Ak-521, collected from the northeastern outer shelf of the Black Sea. A total of 37 ostracod species are recorded in the fossil assemblages, with 2 related to freshwater/oligohaline environments, 23 from Caspian-type environments, and 12 from environments similar to the Mediterranean. Three distinct assemblage zones are identified from the Caspian type dominating in the early Holocene up to 7.4 cal ka BP, a mixed assemblage of Caspian type and Mediterranean type from 7.4 to 6.8 cal ka BP, and a progressive dominance of Mediterranean species from 6.8 cal ka BP. It is very likely that the dominant control of ostracod species occurrence during the period up to ~6.8 cal ka BP is salinity. A range of factors including temperature, biotope, and sedimentation rates influenced the species distribution over the last 6.8 cal ka BP.