Species in Lecanicillium are pathogens that parasitize various arthropods, nematodes, and other fungi. In an investigation of intestinal fungi associated with Marmota monax in China, three strains belonging to the genus Lecanicillium were isolated from the fresh fecal samples. Based on multi-locus phylogenetic analysis of the combined sequences (ITS, LSU, SSU, TEF, RPB1 and RPB2) and morphological characteristics, all species in Lecanicillium were well-separated. The three intestinal strains were assigned to a new species described as L. coprophilum in this paper. The new species differs morphologically from other Lecanicillium species by its dimensions of conidiogenous cells and conidia, the shape of conidia, dictyochlamydospores and swollen hyphae. The differences of L. coprophilum from other Lecanicillium species and closely related taxa are briefly discussed.