Ganoderma is a white-rot fungus with a cosmopolitan distribution and includes several economically important species. This genus has been extensively researched due to its beneficial medicinal properties and chemical constituents with potential nutritional and therapeutic values. Traditionally, species of Ganoderma were identified solely based on morphology; however, recent molecular studies revealed that many morphology-based species are conspecific. Furthermore, some type species are in poor condition, which hinders us from re-examining their taxonomic characteristics and obtaining their molecular data. Therefore, new species and fresh collections with multigene sequences are needed to fill the loopholes and to understand the biological classification system of Ganoderma. In a survey of Ganoderma in Guizhou Province, southwest China, we found a new species growing on soil and, herein, it was identified by both morphology and phylogenetic evidence. Hence, we propose a new species, Ganoderma ovisporum sp. nov. This species is characterised by an annual, stipitate, laccate basidiome, with a red–brown to brownish-black pileus surface and pale white pores, duplex context, clavate pileipellis terminal cells, trimitic hyphal system, ellipsoid basidiospores with dark brown eusporium bearing coarse echinulae and an obtuse turgid appendix. Phylogenetic analyses confirmed that the novel species sisters to G. sandunense with high bootstrap support. Furthermore, the RPB2 sequence of G. sandunense is supplied for the first time. Notably, we re-examined the type specimen of G. sandunense and provide a more precise description of the duplex context, pileipellis terminal cells and basidia. All species collected are described and illustrated with coloured photographs. Moreover, we present an updated phylogeny for Ganoderma, based on nLSU, ITS, RPB2 and TEF1-α DNA sequence data and species relationships and classification are discussed.