The Sea of Galilee is the one and only large freshwater or slightly oligohaline natural lake in the Levant, and it therefore represents an important aquatic habitat in the region that also provides invaluable ecosystem services for the local communities. To improve our knowledge of the lake’s ecosystem and the use of disarticulated ostracod valves and preserved carapaces, micro-crustacean remains commonly used in palaeolimnology and palaeoceanography, as proxies for palaeoenvironmental reconstructions, and to examine the post-mortem dispersal of ostracod remains, 68 surface-sediment samples were collected from the lake floor in 2012 and analysed for the ostracod assemblages. Both, the noded and smooth, forms of Cyprideis torosa dominate in the Sea of Galilee, with the former more abundant than the latter. Relatively abundant and found at half of the 68 sampling locations or more, are also Ilyocypris hartmanni, I. cf. nitida, Darwinula stevensoni and Neglecandona angulata. In addition, ten less abundant ostracod taxa were recorded in the lake. Of all 15 taxa recorded in our study, ten were apparently also recorded in a study of the Sea of Galilee’s ostracod fauna conducted already in the 1960s. The newly recorded five taxa are relatively rare, and they were mostly found in the region of the Jordan River delta or near the southeastern shore of the lake which were not included in the survey of the 1960s. Thus, there is no evidence for a significant change in the ostracod fauna of the lake over the last half-century. In comparison to the ostracod assemblage from a late Pleistocene archaeological excavation site at the southwestern margin of the lake, the assemblage from the recent survey is slightly less diverse, probably as a result of the long duration of ca. 5000 years integrated by the sedimentary section of the archaeological site and also due to nearby freshwater inflows from which valves and carapaces were probably washed to the site’s location. Our study also shows that ostracod valves and carapaces are typically relatively abundant in most of the surface-sediment samples collected from locations at 18 m or shallower. In contrast, very few valves and carapaces were recorded at depths greater than 18 m, which is a zone affected by seasonal anoxia in the Sea of Galilee. These few ostracod remains were apparently transported by currents and waves to the central, deeper part of the lake, but their low number shows that such post-mortem dispersal of ostracod remains is insignificant in the deeper part of the lake. Thus, our study provides support for palaeoenvironmental and palaeoclimate reconstructions based on ostracod records from single sediment cores obtained from depths unaffected by post-mortem transport and seasonal or permanent anoxia.