The influence of Fosetyl-Al and Metalaxyl on the diversity of arbuscular mycorrhizal fungi (AMF) was evaluated on naturally established citrus plants. Thirteen AMF species were recovered from rhizospheres of Citrus sinensis/C. limon treated or not with Fosetyl-Al and/or Metalaxyl. Spores of AMF were obtained from 100 g of rhizospheric soil at two sites in São Paulo state, Brazil. The soil samples were treated by the wet-sieving technique and the spores were quantified and identified. The number of spores was low at both sites. Fosetyl-Al reduced the number of spores and the diversity of AMF in one site but not in the other. Metalaxyl at low concentration increased the diversity of species in some experiments, but at higher concentration it tended to reduce the number of spores of AMF. Scutellospora was the genus that presented the largest number of species (7) followed by Acaulospora (3), Glomus (2) and Gigaspora (1). Gigaspora ramisporophora was the dominant species in one site, Glomus macrocarpum and Scutellospora gilmorei were dominant at the other.