The temporal and spatial dynamics of arbuscular mycorrhizal fungi (AMF) were investigated in Indian Thar Desert. Soil samples under Mitragyna parvifolia were collected from July 2003 to June 2004. AMF colonization and spore density were used to compare the responses of AMF to different abiotic parameters. The mean percent colonization and spore density of AMF reached maximal values in rainy and summer seasons, respectively. Vesicular and hyphal colonizations were positively correlated with soil organic carbon content. AMF spore density was positively correlated with soil pH and negatively correlated with Olsen P content. A high Shannon–Weiner diversity index of AMF was observed in Thar Desert. A total of fifteen AMF species were associated with M. parvifolia. Percent spore density and species richness suggest that the genus Glomus was the predominant AMF under Thar Desert environment. The reasons for the observed variations are discussed.