The micromycete complex population size and taxonomic structure is determined for sediments (bottom soils) of the White Sea; species actively functioning in the littoral zone and at depths of 10–30 m are identified. The bottom-soil fungi population is pretty low (hundreds to several thousand colony-forming units (CFUs) per 1 g), while the species diversity is quite rich. In total, 70 species are identified; 90% of those are Ascomycota anamorphs (Capnodiales, Eurotiales, Hypocreales, Pleosporales, Saccharomycetales, and Incertae sedis), Zygomycota (Mucoromycota) (Mucorales and Umbelopsidales orders) constituted (8%), and the share of Basidiomycota (Agaricales order) is 2%. The actively functioning bottom-soil fungi are identified on the basis of their ability to develop on organic substrates (starch, cellulose, chitin, and pieces of laminaria thallus) and grow on seawater media at low temperatures and varying oxygen levels, i.e., under conditions similar to those observed in the studied ecotope. This fungi group includes some 20 species: Paradendryphiella salina, Acremonium tubakii, A. potronii, Pseudeurotium hygrophilum, Pseudogymnoascus pannorum, Emericellopsis sphaerospora, Oidiodendron periconioides, Parengyodontium album, Lecanicillium muscarium, and representatives of genera Tolypocladium and Sarocladium. These species are typical for marine and cold habitats; some of them are well-known chitinolytics and associates of insects and algae, and many of them are able to grow in anaerobic conditions. For some of the species (Aspergillus brasiliensis, A. sydowii, Cladosporium cladosporioides, Emericellopsis sphaerospora, Oidiodendron periconioides, Pseudeurotium hygrophilum, Tolypocladium cylindrosporum, T. tundrense, Umbelopsis vinacea, Penicillium spp., and Talaromyces spp.), this ability was discovered for the first time. Further studies are required to obtain detailed ecophysiological descriptions of marine isolates of species actively functioning in the bottom soils.