Multiple species of arbuscular mycorrhizal fungi (AMF) colonize roots of an individual plant species but factors which determine the selection of a particular AMF species in a plant root are unknown. The present work analysed the effects of drought, flooding and optimal soil moisture (15–20 %) on AMF community composition and structure in Sorghum vulgare roots, using PCR-RFLP. Rhizophagus irregularis and rhizosphere soil (mixed inoculum) of Heteropogon contortus, collected from the Delhi ridge, were used as AMF inocula. Soil moisture functioned as an abiotic filter and affected AMF community assembly inside plant roots by regulating AMF diversity. Roots of plants in flooded soils had lowest AMFdiversity whilst root AMF diversity was highest under the soil moisture regime of 15–20 %. Although plant biomass was not affected, root P uptake was significantly influenced by soil moisture. Plants colonized with R. irregularis or mixed AMF inoculum showed higher root P uptake than non-mycorrhizal plants in drought and control treatments. No differences in root P levels were found in the flooded treatment between plants colonized with R. irregularis and non-mycorrhizal plants, whilst under the same treatment, root P uptake was lower in plants colonized with mixed AMF inoculum than in non-mycorrhizal plants.