Taxonomic and phylogenetic studies on the Antrodia heteromorpha complex in China were carried out. Antrodia subserpens sp. nov. is described and illustrated. Both the morphology and phylogenetic analysis support this new species. Morphologically, it is characterized by annual, resupinate to effused-reflexed basidiocarps, a dimitic hyphal system with clamped generative hyphae, clavate cystidioles, and ellipsoid to oblong ellipsoid basidiospores; moreover, it causes a brown rot. Molecular data suggested a close relationship between A. subserpens and A. serpens, but the former has slightly smaller pores and shorter basidiospores. Morphologically, A. subserpens is similar to A. tanakae, but separates by its smaller pores and wider basidiospores. An identification key to species of the A. heteromorpha complex is provided.