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Ganoderma is a large and diverse genus containing fungi that cause white rot to infect a number of plant families. This study describes G. phyllanthicola and G. suae as new species from Southwest China, based on morphological and molecular evidence. Ganoderma phyllanthicola is characterized by dark brown to purplish black pileus surface with dense concentric furrows, pale yellow margin, irregular pileipellis cells, small pores (5–7 per mm) and ellipsoid to sub-globose basidiospores (8.5–10.0 × 6.0–7.5 µm). Ganoderma suae is characterized by reddish brown to oxblood red pileus surface and lead gray to greyish-white pore surface, heterogeneous context, wavy margin and almond-shaped to narrow ellipsoid basidiospores (8.0–10.5 × 5.0–7.0 μm). The phylogeny of Ganoderma is reconstructed with multi-gene sequences: the internal transcribed spacer region (ITS), the large subunit (nrLSU), translation elongation factor 1-α gene (TEF-1α) and the second subunit of RNA polymerase II (RPB2). The results show that G. suae and G. phyllanthicola formed two distinct line-ages within Ganoderma. Descriptions, illustrations and phylogenetic analyses results of the two new species are presented. [ABSTRACT FROM AUTHOR]