Pyrola japonica, an Ericaceae, is a mixotroph growing on forest floors, obtaining carbon (C) from both photosynthetic and root-associated mycorrhizal fungal pathways. The mycorrhizal community structures of the plant are well characterised and are dominated by Russulaceae fungi. However, the mechanism of its C acquisition is not well understood. The aim of this study was to identify mycorrhizal fungal communities that are directly involved in C acquisition. We repeatedly applied a fungicide (Benomyl) solution to soils around P. japonica plants in a broad-leaved forest in central Japan to disturb fungal associations near their roots. After fungicide treatment, P. japonica roots were collected and subjected to next-generation sequencing, focusing on the ITS2 region, to infer taxonomic identities. The leaves and seeds of the plants were analysed for C stable isotope ratios. The rate of mycorrhizal formations and α-diversity did not significantly change by the fungicide treatments. Irrespective of the treatments, more than 80% of the detected mycorrhizal taxa were assigned to Russulaceae. For δ13C values, leaves and seeds in the fungicide were significantly lower than those of the other treatments. Our results suggest that the fungicide did not affect mycorrhizal communities, but likely disturbed mycorrhizal fungal pathways via extraradical hyphae, which may result in a relative increase in its own photosynthetic pathways.