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A field study of traditional agroforestry systems in six districts of the and and semiarid zones of Rajasthan was undertaken where annual rainfall varied from 140 to 1000 mm and soil types ranged from course fine sand in Jaisalmer to clay loams in Kota. The field investigation showed that Glomus, Gigaspora and Sclerocystis were the genera of arbuscular mycorrhizal fungi present in the neem-based agroforestry system. Among the three genera, Glomus occurred most frequently, with 15 species of Glomus, 3 of Gigaspora and 2 of Sclerocystis observed. Glomus fasciculatum was the predominant arbuscular mycorrizal (AM) fungus infecting neem. Of the six districts surveyed, five had the highest diversity index of G. fasciculatum, at sites where Sclerocystis species were present in districts of low rainfall, viz. Jaisalmer, Barmer and Jodhpur. The maximum spore density in the neem tree rhizosphere was in Jodhpur and the minimum in Kota. However, in the crop rhizosphere the maximum was in Jaipur and the minimum in Jaisalmer. At all sites, spore density was greater in tree and crop rhizospheres than in the soils of uncropped sites. Infection was higher in tree roots than crop roots. The factors Fe, Zn and maximum temperatures affected the AM fungal populations significantly in the neem rhizosphere. In associated crop rhizospheres electrical conductivity (EC), organic C, Fe. P. CaCO3, maximum temperature, rainfall and humidity affected the AM populations. The results indicate that G. fasciclatum was the dominant stable AM fungus in these areas. (C) 2004 Elsevier B.V. All rights reserved.