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Improving maize yield is an objective of utmost importance for food security in Uganda. In the evaluation of soil microorganisms in crop production, it is important to assess the composition and diversity of the arbuscular mycorrhizal fungi (AMF) species in different agroecosystems. AMF play an important role in improving crop growth and yield. We present a study of the morphological diversity of native AMF species associated with the rhizosphere of maize in two locations in eastern Uganda (the Amuria and Serere districts). The effects of soil chemical properties on this diversity are also assessed. AMF diversity is assessed by the morphological identification of the spores extracted from soils samples by the wet sieving method. Spores abundance, species richness, and diversity are determined. A total of 19 AMF morphotypes distributed in 7 genera (Gigaspora, Scutellospora, Glomus, Acaulospora, Archaeospora, Entrophospora, and Paraglomus) are observed. Glomus species are abundant in all sites. Spore densities are higher in Amuria than in Serere. Soil pH, CEC, and phosphorus content influence AMF distribution. Finding the species in various agroecological environments indicates that they are adapted to the environments. Maize grown in eastern Uganda is associated with a diversity of AMF that could be selected as bio-fertilizers to improve crop production. [ABSTRACT FROM AUTHOR]