Species of Amauroderma and Ganoderma (Ganodermataceae) have been widely used as traditional medicines in Asia over many centuries. The genera are widely researched, owing to their beneficial medicinal properties and chemical constituents with potential nutritional and therapeutic uses. There are, however, taxonomic confusions surrounding the species in these genera, whose circumscription is often unclear. We surveyed species of Amauroderma and Ganoderma in Hainan Island in Southern China. In this paper, we provide data on 15 species found in the Wuzhishan and Jiangfengling mountains on the island. One species named Ganoderma ellipsoideum Hapuar., T.C. Wen & K.D. Hyde, sp. nov. is new to science and introduced with evidence from morphology and molecular analysis. The other species collected are described with photographs and compared with similar taxa. We provide a phylogeny for the two genera based on ITS sequence data and the taxonomic status of the species is briefly discussed.