Qatar is largely characterized by a hyper-arid climate and low soil fertility which create a stressful soil environment for arbuscular mycorrhizal (AM) fungi. In a study of AM fungal communities and their relationship with soil chemical characteristics, we used a high-throughput sequencing technique to explore AM fungal diversity and community composition in different habitats across Qatar. We identified a total of 79 AM fungal taxa, over 77% of which were species from the Glomeraceae family. The lowest AM fungal diversity was observed in saltmarsh and in one rawdha site, while the highest richness, effective number of species, and diversity were observed in rawdha and sabkha communities. NMDS and multiple regression analyses showed that AM fungi were negatively correlated with soil pH and TC, but positively correlated with K and NO3-. AM fungi also were positively correlated with Cd, with the latter suggesting that very low levels of heavy metals may not always be harmful to AM fungi. These findings provide baseline information on AM fungal assemblages and the chemical drivers of diversity across communities in Qatar.