Here, Podospora leporina was isolated and cultured from Cypripedium guttatum Sw. (spotted lady’s slipper), which was designated as an endangered wildlife class 1 by the Ministry of Environment. Further, Podospora sp., which is found in Calanthe discolor Lindl. (Japanese hardy orchid) root is recorded as an endophytic fungus in Jeju Island, Korea. However, there is no existing record of Podospora spp. Thus, in this study, we analyzed the morphological characteristics and two molecular markers, internal transcribed spacer (ITS) and large ribosomal subunit (LSU), of P. leporina and compared these data with other relative species. Consequently, this endophytic fungal species was confirmed as an unrecorded species in Korea, so we presented cultural characteristics and microstructures, such as the conidia of P. leporina.