The deviation of conventional fungal niches is an important factor in the implications of hidden fungal diversity and global fungal numbers. The Xylariomycetidae (Sordariomycetes, Ascomycota), which is also referred to as xylarialean taxa, has a wide range of species that demonstrate a high degree of variation in their stromatic characteristics, showing either conspicuous or inconspicuous forms. In this study, samples were collected while focusing on temporal and spatial parameters and substrate characteristics. Based on internal transcribed spacer (ITS), 28S large subunit rDNA (LSU), RNA polymerase II second largest subunit (RPB2), and β-tubulin (TUB2) multigene phylogeny and morphology, five new species are introduced as Muscodor brunneascosporus, M. lamphunensis (Xylariaceae), Nigropunctata hydei, N. saccata (Incertae sedis), and Xenoanthostomella parvispora (Gyrotrichaceae). Plant substrates in the early stages of decay and attached to the host were feasible sample niches, with an emphasis on the collection of inconspicuous, hidden xylarialean species. The appearance of inconspicuous saprobic xylarialean forms during the rainy season may be linked to the change in nutritional mode, from endophytic mode during the dry season to saprobic in the wet. Therefore, it would be fascinating to concentrate future research on how seasonal fluctuations affect nutritional mode shifts, especially in northern Thailand, which would provide the optimal spatial characteristics. In order to establish a comprehensive linkage between endophytic and saprobic modes, it is imperative to have a substantial representation of endophytic isolate sequences resembling inconspicuous xylariaceous fungi within publicly accessible databases.