Microbiota of the deep caves has been poorly explored. The most relevant issues of the caves biodiversity are the sources of the microorganisms' propagules and characteristics of autochthonous microbiota. The investigation presents the assessment of microbiota biodiversity from the Dzou cave (Western Caucasus). The aim of the study was to identify the species composition of micromycetes and phototrophs of the cave and to assess the sanitary-indicative microbiota in different habitats depending on the anthropogenic load. Microscopic and cultural methods were used to identify the microbiota from the entrance zone of the cave, as well as from aquatic and terrestrial habitats of the unlit deepest parts of the cave. The analysis of the phototrophic communities composition developed in the entrance area of the cave was carried out, 22 species were identified, among which cyanobacteria prevailed. The biodiversity of micromycetes was determined: 48 species were identified in the entrance zone, 60 species - in the dark zone of the cave. Comparison of the species composition of the dark and illuminated zones of the cave showed that in addition to species Humicola grisea, Hemicarpenteles ornatus and Alternaria sp., all species of entrance area are found in the unlit part of the cave. Representatives of genus Penicillium and Aspergillus were dominants. Revealed increase of the micromycetes and bacteria number was driving by increase in the level of anthropogenic load, especially in places of tourist camps. It was noted that the propagules of phototrophs are present in the cave substrates even at great depth, excluding some water samples, which may indicate the periodic drift of propagules or anthropogenic factor. The largest number of micromycetes species was detected in the clay deposits and rock samples. The least number of species was isolated from the water streams of the cave. A large number of micromycetes propagules was found in substrates near tourist camps, but their biodiversity was lower than in cave soils. © Published under licence by IOP Publishing Ltd.