For the first time, the composition of micromycetes communities was investigated in both photic and aphotic entrance zones of seven caves in Montenegro: Obodska Pećina, Golubinja Pećina, Veluštica Pećina, Vrbacka jama, Jama ER-1, Njegoš Pećina, and an unnamed cave. In total, 72 species of micromycetes were identified: 46 species from illuminated photic zones of the caves, including 43 species on phototrophs, 10 species from the air, 15 species on substrates, and 50 species from unlit aphotic zones, including 35 species from the air and 37 species on substrates. The most frequently isolated species were Acrodontium salmoneum, Aureobasidium pullulans, Cladosporium oxysporum, Mucor racemosus f. racemosus, Penicillium chrysogenum, and Rhizopus stolonifer. The similarity between micromycetes composition of different biotopes was evaluated using the Jaccard index and cluster analysis. The greatest similarity was observed in the communities isolated from the air of the photic zones of the caves. © 2020, Springer Nature B.V.