Over the past two decades, hypoxylaceous specimens were collected from several sites in Thailand. In this study, we examined their affinity to the genus Pyrenopolyporus using macroscopic and microscopic morphological characters, dereplication of their stromatal secondary metabolites using ultrahigh performance liquid chromatography coupled to diode array detection and ion mobility tandem mass spectrometry (UHPLC-DAD-IM-MS/MS), and molecular phylogenetic analyses. We describe and illustrate five novel species and a new record for the country, present multi-locus phylogenetic analyses that show the distinction between the proposed species, and provide proteomic profiles of the fungi using matrix associated laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF/MS) for the first time. Based on our findings, this strategy is useful as a complementary tool to distinguish species between Daldinia and Pyrenopolyporus in a consistent way with the phylogenetic analysis.