In plant roots, arbuscular mycorrhizal fungi (AMF) are the most prevalent microsymbionts, and thereby provide many key ecosystem services to natural and agricultural ecosystems. Despite AMF’s significance for the environment and the economy, little is known about the mycorrhizal inoculum potential and diversity of AMF associated with orphan African cereal crops, specially fonio millet (Digitaria exilis stapf.) under field conditions. We hypothesized that the type of fonio millet agroecosystem influences the AMF density and distribution in soils. We therefore, assessed the inoculum potential, density and diversity of AMF spores and soil enzyme activities in five fonio millet agroecosystems belonging to three climatic zones (Sudanian, Sudano-Sahelian and Sudano-Guinean). By combining AMF spore identification from field-collected soils and trap culture, 20 species belonging to 8 genera (Acaulospora, Ambispora, Dendiscutata, Gigaspora, Glomus, Racocetra, Sclerocystis and Scutellospora) were identified. Glomus was the most represented genus with 8 species, followed by Gigaspora (5 species) and Acaulospora (2 species); the remaining genera were each represented by one species. Except for Ambispora which was not found in the Sudanian area, all genera occurred in the three climatic zones. The abundance and diversity of AMF species and FDA-hydrolytic and phosphatase activities varied between fonio millet agroecosystems as well as between climatic zones. Soil pH and soil texture were the variables that best explained the density and distribution of AMF spores. Our results contribute to paving the way towards the development of microbial engineering approaches for agronomic improvement of fonio millet.