Assessment of microbial diversity and understanding factors underlying species distribution are fundamental themes in ecology. Arbuscular mycorrhizal fungi (AMF) are key actors among soil microbial communities, forming a beneficial association with most crops and horticultural plants. However, for maize, data on AMF species diversity in east Africa tropical agroecosystems is totally nonexistent. This research was carried out to assess the morphological diversity of native AMF species associated with the rhizosphere of maize in eastern Uganda and to examine the effects of soil chemical properties on this diversity. Soil samples were collected from two sites (in Amuria and Serere districts). Spores were extracted from the field soils by the wet sieving method, counted, and morphologically identified. Spores occurrence, abundances, species richness, and diversity were determined. A total of 49 AMF morphotypes distributed in 7 genera (Gigaspora, Scutellospora, Glomus, Acaulospora, Archaospora, Entrophosporaa, and Paraglomus) were obtained with the majority being from Gigasporaceae, Acaulosporaceae, Paraglomeraceae, and Glomeraceae families. All morphospecies were ubiquitous in all the sites. Spores densities were higher in Amuria than in Serere. Soil pH and phosphorus content influenced AMF distribution. Finding the species in a wide range of physicochemical environments indicates that they are adapted to those environments. Maize grown in eastern Uganda is associated with a diversity of AMF which could be selected as bio-fertilizer to contribute to improving crops production.