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<i>Hydnobolites</i> is an ectomycorrhizal fungal genus with hypogeous ascomata in the family <i>Pezizaceae</i> (<i>Pezizales</i>). Molecular analyses of <i>Hydnobolites</i> using both single (ITS) and concatenated gene datasets (ITS-nLSU) showed a total of 223 sequences, including 92 newly gained sequences from Chinese specimens. Phylogenetic results based on these two datasets revealed seven distinct phylogenetic clades. Among them, the ITS phylogenetic tree confirmed the presence of at least 42 phylogenetic species in <i>Hydnobolites</i>. Combined the morphological observations with molecular analyses, five new species of <i>Hydnobolites translucidus</i> sp. nov., <i>H. subrufus</i> sp. nov., <i>H. lini</i> sp. nov., <i>H. sichuanensis</i> sp. nov. and <i>H. tenuiperidius</i> sp. nov., and one new record species of <i>H. cerebriformis</i> Tul., were illustrated from Southwest China. Macro- and micro-morphological analyses of ascomata revealed a few, but diagnostic differences between the <i>H. cerebriformis</i> complex, while the similarities of the ITS sequences ranged from 94.4 to 97.2% resulting in well-supported clades.