The paper provides data on aphyllophoroid fungi of the planned protected area Shuya River Mid-course situated in the south of the Republic of Karelia. Forests in the area are spruce stands and mixed spruce-pine, spruce-deciduous stands 90–160 years old. The checklist of aphyllophoroid fungi includes 128 species. Ten species are novel for the Karelia olonetsensis biogeographic province (Athelia epiphylla, Byssomerulius albostramineus, Ceriporia reticulata, Gloeocystidiellum porosum, Kurtia argillacea, Mucronella calva,
Phlebia cretacea, P. lilascens, Tomentella coerulea, T. lapida). Locations of 3 species of aphyllophoroid fungi (Diplomitoporus crustulinus, Lentaria afflata, Tomentella crinalis) and 1 agaricoid species (Stropharia aeruginosa) listed in the Red Data Book of the Republic of Karelia (2020) as well as 13 indicator and 9 specialized species of old-growth forests have been found in the study area. The list includes data on their habitats, substrates and frequency. The substrate for 71 species was coniferous wood and 66 species were recorded from deciduous trees. The greatest numbers of fungal species were found on spruce (68), aspen (46), birch (31), and pine (25). Specimens are kept in the herbarium of the Karelian Research Centre (PTZ). The information obtained can be used to substantiate the planned protected area and serves as the background for further mycological studies.