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Mucorales comprises fungi commonly isolated from soil, herbivore dung, and plant debris. Surveys in the semi-arid northeastern region of Brazil revealed 20 species of Mucorales, although this does not reflect the potential richness of these fungi in the Caatinga, the main domain of the region. Therefore, the aim of the present study was to compare the richness, diversity, frequency, and distribution of Mucorales from natural and degraded semi-arid soils of the Catimbau National Park, Pernambuco State, Brazil, and to provide a taxonomic key for the species found in the studied soils. Six samplings were performed in three natural areas with the following vegetation types: Carrasco, Sandy Caatinga, and Caatinga s. s., as well as in an area of Caatinga s. s. under anthropic use. Thirteen taxa of Absidia, Cunninghamella, Gongronella, Lichtheimia, Mucor, Rhizopus, and Syncephalastrum were identified. Both richness and diversity were distinct among vegetation types. Rhizopus microsporus was the most common species. Soils from Carrasco exhibited a highest diversity and richness. The anthropic effects explain the low richness and diversity found on Caatinga s. s. Two species were reported for the first time in the Caatinga domain and a new species of Absidia was recorded.