We demonstrate the presence of unique, previously unknown phylogenetic lineages of Amoebozoa in the deep-sea bottom sediments. At the same time, some of these lineages are currently represented by multiple species, and their deep-sea members are closely related to the species isolated from shallower habitats. There are also examples of deep-sea amoebae lineages containing very closely related species isolated from distant areas of the ocean. In most cases, comparison between water column, bottom sediments, as well as deeper and shallower habitats allows a conclusion that the species composition in the sampled habitats is mainly determined by the habitat type (e. g., bottom sediments vs. water column), that may, in turn, determine the amount and type of substrates for amoebae to dwell on. The diversity of species on the bottom sediment surface decreases with increasing depth, which is likely to be determined by the factors, indirectly influenced by the depth, such as temperature, salinity and the amount of ava