The relevance of the study is driven by the growing interest in energy crops not only as a source of biomass, but also as a factor influencing the biological and phytosanitary status of soil. This paper presents the results of a study of the genus-level structure of soil micromycete communities in grey forest soil under long-term cultivation of perennial energy crops in the western region of Ukraine. The object of the study was the effect of long-term cultivation of Silphium perfoliatum L., Sida hermaphrodita (L.) Rusby, and Miscanthus × giganteus on the genus-level structure of soil micromycetes in grey forest soil; soil under a traditional field crop rotation was used as the control. Soil analysis was carried out on the basis of phytopathological laboratory examinations, including the determination of the abundance of fungi belonging to the genera Fusarium, Penicillium, Trichoderma, Aureobasidium, and Gliocladium. It was established that the composition of soil micromycetes depended on the cultivated crop species. The highest abundance of Fusarium was detected in soil under Silphium perfoliatum, whereas under Miscanthus × giganteus it was close to the control level. The highest abundance of Penicillium was recorded under Sida hermaphrodita and Silphium perfoliatum. The greatest development of Trichoderma was observed under Miscanthus × giganteus, whereas fungi of this genus were not detected in soil under Silphium perfoliatum. Aureobasidium was detected only in the control and under Sida hermaphrodita, while the highest abundance of Gliocladium was found under Sida hermaphrodita. The results indicate that long-term cultivation of perennial energy crops causes species-specific changes in the structure of soil micromycetes. Among the studied energy crops, Miscanthus × giganteus had the most favorable effect on the formation of soil micromycete communities, since soil under this crop combined a low abundance of Fusarium with a very high abundance of Trichoderma. In contrast, Silphium perfoliatum proved to be the least favorable variant, as soil under this crop showed a high abundance of Fusarium and the absence of Trichoderma.