For the first time, associations of microscopic fungi and nematodes were found in bottom sediments, periphyton and on driftwood in the Black Sea. Antagonistic relationships between microscopic fungi and nematodes are considered: fungi and fungal-feeding nematodes; nematophagous fungi and nematodes. In laboratory conditions, fungal-feeding nematodes remain viable for 1.5 to 9 months in the presence of 22 species of micromycetes from 20 genera, 11 families, 8 orders, 5 classes, and the phylum Ascomycota. The representatives of the family Halosphaeriaceae dominated in terms of the number of species in the species composition of fungi (9). Five species of fungi were found as part of the associations in bottom sediments and 21 species on driftwood. It is proved that the fruiting bodies of ascomycetes Corollospora maritima, C. trifurcata, Halosphaeriopsis mediosetigera with spores can be the only food source for nematodes Viscosia minor, Oncholaimus sp., Monhystera sp. Micromecetes Corollospora maritima, C. trifurcata, Halosphaeriopsis mediosetigera prevailed in the composition of associations on the driftwood, 16.67–20.83%. The paper presents 19 fungi which were for the first time identified in such associations. Epi- and endobiont fungi were detected during microscopic analysis of nematodes after their fixation and making constant microscopic preparations, but it was impossible to identify exactly their taxonomic affiliation. The nematode Anticoma pontica from the fouling in an underground canal inside Mount Tavros (Balaklava Bay, Sevastopol) was affected by a fungal ectoparasite similar to Drechmeria sp. (phyllum Ascomycota). The nematode Axonolaimus setosus from the sediments on the shelf of the western Crimea from a depth of 83.5 m was apparently infected with a fungal-like organism from the phylum Oomycota. Individuals of A. setosus with hyphae of fungi in the inner cavity and on the cuticle (Fungi sp.) were found in the area of the Bosphorus Strait at a depth of 250 m (hydrogen sulfide zone). The state of morphological and anatomical structures of worms indicates that they were affected by fungi during their lifetime.