Two novel species of Lyophyllum are proposed based on morphological and phylogenetic investigations. Lyophyllum bulborhizum sp. nov. has abundant black scales on the surface, is a dry, dark grey at the center, grey at the margin, has a clear bulbous stipe base, and has a narrowly cylindrical or narrowly clavate pleurocystidia and cheilocystidia. Lyophyllum nigrum sp. nov. is tufted and has a dark grey pileus and subclavate, a greyish green-to-olive stipe, and a narrowly cylindrical or narrowly clavate pleurocystidia and cheilocystidia. In addition, L. rhombisporum is described with morphology and phylogeny and compared with the type species. Molecular analyses employing internal transcribed spacer (ITS) sequences strongly support the two new species to be unique in the genus Lyophyllum. Full descriptions, colour photos, illustrations, and phylogenetic analyses results of the two new taxa and the known taxon are presented in this study.