Species of Mucor are known to be saprophytes that can be found in all parts of our environment. The Mucor is the largest genus within order Mucorales with more than 90 currently accepted species. Several Mucor species have important biotechnological applications and are used to produce fermented foods in Asia. It also includes some opportunistic human pathogens. However, the knowledge about the taxonomy of genus Mucor in Korea is still limited. The aim of this study was to characterize Mucor species isolated from different niches and host, i.e., soil, freshwater, seed, and invertebrates. A total of 39 Mucor isolates were obtained. Combining morphological, physiological characters and phylogenetic analyses of the internal transcribed (ITS) regions and ribosomal DNA large subunit (LSU), these isolates were identified as 15 species of Mucor. Nine species were represented as new species, two as new records, and four as new host records in Korea. Herein, detailed descriptions, illustrations and phylogenetic trees are provided. Our study contributes to the expansion of knowledge on the taxonomy and diversity of Mucor species in Korea.