Fungi plays a central role in lignin decomposition in leaf litter. Selective lignin decomposition by fungi, which leads to the bleaching of leaf litter, stimulates the mass loss of litter as lignin is known as a rate-limiting factor of decomposition. Previous studies have shown that fungi in Xylariaceae and Hypoxylaceae (Ascomycota) were frequently isolated from bleached parts of leaf litter collected across Japan and are involved in lignin decomposition. However, few studies have examined the phylogenetic diversity of Xylariaceae and Hypoxylaceae associated with the bleached leaf litter. In this study, we isolated Xylariaceae and Hypoxylaceae from bleached parts of leaf litter of seven tree species in Okinawa (subtropical forest) and two tree species in Nagano (cool-temperate forest) in Japan and evaluate their taxonomic and phylogenetic diversity. The 266 strains isolated were classified into 44 operational taxonomic units (OTUs) at the 97% sequence similarity threshold based on the rDNA ITS sequences. The numbers of OTU was not significantly different between the nine tree species, whereas the OTU composition significantly differed among the tree species. We constructed a maximum likelihood tree of 44 OTUs to calculate three common metrics for the phylogenetic alpha diversity, namely Faith’s phylogenetic diversity (PD), mean pairwise distance (MPD) and mean nearest taxon distance (MNTD). Faith’s PD, MPD, and MNTD were lower in fungal assemblages of subtropical leaves than in those of cool-temperate leaves, indicating the phylogenetic clustering versus phylogenetic overdispersion of xylariaceous and hypoxylaceous fungi in subtropical and cool-temperate leaves, respectively.