Yellow rot, caused by an ascomycetous fungus having a distinctive arthroconidial anamorph, is the most destructive disease of cultivated Ganoderma lucidum in Korea, but the identity of the yellow rot pathogen (YRP) remains uncertain. Isolates have been identified as Xylogone sphaerospora (with putative anamorph Sporendonema purpurascens) or as Arthrographis cuboidea. Therefore we used morphological features, pathogenicity tests and phylogenetic analyses of DNA sequences from the nuclear ribosomal genes, including partial small subunit and internal transcribed spacer regions, and from the gene encoding RNA polymerase second largest subunit to evaluate the relationship between YRP isolates and these species. YRP isolates formed a distinct subgroup within a clade that included X. sphaerospora, A. cuboidea and Scytalidium lignicola, the type species of Scytalidium, but the disposition of the clade within the Leotiomycetes was uncertain. We describe Xylogone ganodermophthora sp. nov. and Scytalidium ganodermophthorum sp. nov. for the teleomorph and anamorph of YRP respectively. Arthrographis cuboidea is reclassified as Scytalidium cuboideum comb. nov., and the anamorph of X. sphaerospora is named Scytalidium sphaerosporum sp. nov. In pathogenicity tests only X. ganodermophthora caused disease in Ganoderma lucidum. Amplified fragment length polymorphism analyses showed that X. ganodermophthora populations from diseased fruiting bodies or from oak wood in Korea consisted of two clonal groups.