Zygomycetes are phylogenetically early diverging, ecologically diverse, industrially valuable, agriculturally beneficial, and clinically pathogenic fungi. Although new phyla and subphyla have been constantly established to accommodate specific members and a subkingdom Mucoromyceta, comprising Calcarisporiellomycota, Glomeromycota, Mortierellomycota and Mucoromycota, was erected to unite core zygomycetous fungi, phylogenetic relationships within phyla have not been well resolved. Taking account of the information of monophyly and divergence time estimated from ITS and LSU rDNA sequences, the present study updates the classification framework of the phylum Mucoromycota from the class down to the generic rank: three classes, three orders, 20 families (including five new families Circinellaceae, Protomycocladaceae, Rhizomucoraceae, Syzygitaceae and Thermomucoraceae) and 64 genera. The taxonomic hierarchy was calibrated with estimated divergence times: phylum earlier than 617 Mya, classes and orders earlier than 547 Mya, families earlier than 199 Mya, and genera earlier than 12 Mya. Along with this outline, all genera of Mucoromycota are annotated and 58 new species are described. In addition, three new combinations are proposed. In this study, we update the taxonomic backbone of the phylum Mucoromycota and reinforce its phylogeny. We also contribute numerous new taxa and enrich the diversity of Mucoromycota.

接合菌是系统发育早期分化、生态多样化、具有工业价值、农业有益和临床致病的真菌。尽管新的门和亚门不断被建立以适应特定的成员，并且建立了毛霉亚界，包括钙孢菌门、球囊菌门、被孢霉门和毛霉门，以统一核心接合菌真菌，但门内的系统发育关系尚未得到很好的解决。考虑到ITS和LSU rDNA序列估计的单系和分化时间信息，本研究更新了毛霉菌门的分类框架，从纲到属等级：三纲，三目，20科（包括5个新科） Circinellaceae、Protomycocladaceae、Rhizomucoraceae、Syzygitaceae 和 Thermomucoraceae 科）和 64 个属。分类层次结构是根据估计的分歧时间进行校准的：门早于 617 Mya，纲和目早于 547 Mya，科早于 199 Mya，属早于 12 Mya。除此概要外，还对毛霉菌门的所有属进行了注释，并描述了 58 个新种。此外，还提出了三种新的组合。在这项研究中，我们更新了毛霉菌门的分类骨架并强化了其系统发育。我们还贡献了许多新的分类单元并丰富了毛霉菌门的多样性。