The burgeoning accumulation of genomic data in recent years has revolutionized our understanding of fungal phylogenies and classifications. However, the genomic era also brings new challenges, as phylogenetic incongruences make the appearance of monophyly in some phylogenetic trees questionable. Existing criteria for constructing taxonomic systems, such as diagnostic characters and divergence time, become insufficient to address this challenge. Through order-level analyses of genomic data of the Subkingdom Dikarya within the Kingdom Fungi, we introduce the extended quadripartition internode certainty (EQP-IC) value as a novel criterion for constructing high-level fungal classifications, with a recommended threshold of 0.1 for each taxonomic rank. Suprageneric taxa with an EQP-IC value exceeding 0.1 exhibit reduced topological variation, suggesting a stronger correspondence with natural taxonomic category. This new criterion was also put into practice to investigate the derived suborders of mushroom-forming Agaricales, including three suborders, Agaricineae, Pluteineae, and Tricholomatineae (APT), that had been long-standing problems in phylogenetic analyses. In total, 142 genomes, including 64 newly generated ones, were utilized to reconstruct the phylogenetic relationships and delve into the phylogenetic incongruencies and evolutionary histories of APT. Our data suggested widespread and high-level incomplete lineage sorting (ILS) and introgression/hybridization (IH) present among suborders within the APT. Therefore, a dichotomous phylogenetic tree may not reflect the real relationships among the clades within the APT. Instead, their natural relationships may be reticulate. Three newly named suborders, Amanitineae, Macrocystidiineae, and Omphalinineae are added to the clade including APT. The new combination Baisuzhenia humphreyi, new genus Baisuzhenia, new family Baisuzheniaceae, and new suborder Baisuzheniineae are proposed to accommodate Stereopsis humphreyi, which shows an independent, but close relationship, with the clade formed by the six above-mentioned derived suborders of Agaricales.

Species of Cystolepiota are known as diminutive lepiotaceous fungi with a worldwide distribution. Previous studies revealed that Cystolepiota is not monophyletic and preliminary DNA sequence data from recent collections suggested that several new species exist. Based on multi-locus DNA sequence data (the nuc rDNA internal transcribed spacer region ITS1-5.8S-ITS2, ITS; the D1–D2 domains of nuc 28S rDNA, LSU; the most variable region of the second-largest subunit of RNA polymerase II, rpb2 and a portion of the translation–elongation factor 1-α. tef1), C. sect. Pulverolepiota forms a distinct clade separating from Cystolepiota. Therefore, the genus Pulverolepiota was resurrected and two combinations, P. oliveirae and P. petasiformis were proposed. With the integration of morphological characteristics, multi-locus phylogeny, and information on geography and habitat, two new species, viz. C. pseudoseminuda and C. pyramidosquamulosa, are described and C. seminuda was revealed to be a species complex containing at least three species, viz. C. seminuda, C. pseudoseminuda, and Melanophyllum eryei. In addition, C. seminuda was re-circumscribed and neo-typified based on recent collections.

Species of Micropsalliota generally grow in the tropics and are characterised by small, slender basidiomes, brown basidiospores, and cheilocystidia that vary in shape with capitate or subcapitate apex, and pigmented pileipellis. Based on morphological characters and molecular evidence, here we describe seven new species from southern China, viz. Micropsalliota ferruginea, M. fimbriata, M. gigaspora, M. longicystis, M. nana, M. squarrosa, and M. umbonata. Micropsalliota appendiculata, a species recently described from Vietnam, was first recorded in China. The Maximum likelihood and Bayesian analyses based on multi-locus sequence datasets (the nuc rDNA internal transcribed spacer region ITS1-5.8S-ITS2, nrITS; the D1-D2 domains of nuc 28S rDNA, LSU; partial sequences of the most variable region of the second-largest subunit of RNA polymerase II, rpb2, and a portion of the translation-elongation factor 1-α, tef1) shows that the genus is separated into 11 major clades and subclades. To aid in diagnosis, a key to 32 species of Micropsalliota in China is provided.

The genus Scleroderma contains gasteroid basidiomycetes, which form globose spores with echinulate to reticulate ornamentation on the surface. Based on the morphological observations in combination with molecular data, four new species, S. erubescens, S. separatum, S. squamulosum, and S. vinaceum, were described from Yunnan, southwestern China. Images of fresh basidiomata and scanning electron microscope (SEM) images of basidiospores are provided. Phylogenetic analyses based on ITS sequences show that these four new taxa belong to the Scleroderma section Scleroderma.

Smithiomyces is reported for the first time from tropical regions in China, thus expanding its known native geographic range from the Neotropics to tropical Asia. Phylogenetic evidence from four nuclear loci supports the monophyly of Smithiomyces and a close evolutionary relationship with the nonmonophyletic genera Melanophyllum and Cystolepiota in the Agaricaceae. Detailed morphological descriptions are provided for three newly described species from China: S. asiaticus, S. heterosporus, and S. lepiotoides. Illustrations of fresh basidiomata in the field, line drawings of key anatomical features, microscopic images of anatomical features, scanning electron microscope (SEM) images of basidiospores, and a key to known species of Smithiomyces are also provided.