The influence of the long-term exposure to heavy metal on the soil microbial diversity was explored in soil from six different sites along a pollution gradient near the superphosphate factory, Assiut, Egypt. The biodiversity of microbial populations by means of numbers of colony forming units in 1 g of dry weight soil (CFU g–1) was determined by plate count on appropriate media: fungi on potato dextrose agar (PDA) and bacteria on nutrient agar (NA). Soil heavy metals content (Fe, Mn, Cu, Zn, Cd, Ni, Cr, Pb) and pH were determined. Results indicated that concentrations of some heavy metals recorded high amount in soil samples exposed to pollution and exceeded the maximum allowable limits. It was possible to isolate thirteen mesophilic and five thermotolerant and thermophilic fungal species from contaminated soil samples under study. A total number of nine morphotypes of Arbuscular Mycorrhizal Fungi (AMF) belonging to the families Acaulosporaceae, Glomeraceae and Gigasporaceae were obtained. The mesophilic and thermophilic bacterial populations were different between the soils. Meanwhile, the thermophilic bacterial populations were regularly lower than mesophilic bacterial populations. Combining the information from heavy metal concentrations and microbial diversity data provided an understanding of the impacts of factory pollution on microbial communities.