Hybrid aspen Populus tremula L. × Populus tremuloides Michx. is fast-growing and a potential source of biomass for bioenergy production in Europe. However, knowledge about the phytopathological risks to hybrid aspen clones, particularly about frost crack damage as a possible infection gateway of fungal infections, is scarce. Five clones, represented by 205 trees from three trials in Latvia, were studied; two wood samples (at root collar and 1.3 m height) were obtained from each tree. Wood-inhabiting fungi were isolated and identified by the morphology and sequencing of the ITS region with fungal-specific primers, and fungal communities were compared using PERMANOVA. Fungal communities from trees with stem cracks were richer in species, especially pathogens, and species richness was higher in samples collected at 1.3 m height. Plant pathogens were isolated from 52% of all samples. Soft rot-causing Alternaria and Fusarium were dominant; Alternaria was more common at the height of 1.3 m, while Fusarium was more common at the root collar. White rot fungi were isolated from less than 2% of all samples, indicating a low degree of tree infection in the 15- to 16-year-old plantations. Clonal differences were not significant for fungal communities in general; nevertheless, for the occurrence of the genus Cladosporium, clonal differences were observed. In conclusion, the differences in fungal communities in relation to stem cracks implied only indirect clonal effects on phytopathological risks, emphasizing the resistance to stem cracking as a crucial trait for the sustainability of hybrid aspen plantations.