The order Mucorales, the largest in number of species within the Mucoromycotina, comprises typically fast-growing saprotrophic fungi. During a study of the fungal diversity of undiscovered taxa in Korea, two mucoralean strains, CNUFC-GWD3-9 and CNUFC-EGF1-4, were isolated from specific habitats including freshwater and fecal samples, respectively, in Korea. The strains were analyzed both for morphology and phylogeny based on the internal transcribed spacer (ITS) and large subunit (LSU) of 28S ribosomal DNA regions. On the basis of their morphological characteristics and sequence analyses, isolates CNUFC-GWD3-9 and CNUFC-EGF1-4 were confirmed to be Gilbertella persicaria and Pilobolus crystallinus, respectively.To the best of our knowledge, there are no published literature records of these two genera in Korea.