Display omitted •AMF occurrence, diversity and community composition were investigated in apple roots.•High levels of mycorrhizal colonization were found in 21 South Tyrol apple orchards.•Two molecular methods, PCR cloning and sequencing and PCR-DGGE, were used.•For the first time native AMF in apple roots were identified at the species level.•Geographical area, management and altitude affected AMF diversity in apple roots. Arbuscular mycorrhizal fungi (AMF) are beneficial microrganisms which establish mutualistic symbioses with the roots of most food crops, improving plant performance, nutrient uptake and tolerance to biotic and abiotic stresses. A better understanding of the factors affecting AMF occurrence and diversity is fundamental to implement sustainable agricultural managements effectively profiting from beneficial plant symbionts. Here, we investigated AMF occurrence, diversity and community composition in the roots of apple trees from 21 orchards in South Tyrol, as affected by location, management (organic vs integrated) and altitude, by PCR cloning and sequencing and PCR-DGGE of partial 18S rRNA gene. The screening of 448 clones from 21 clone libraries allowed the identification of 6 native AMF at the species level: Glomus indicum, Sclerocystis sinuosa, Funneliformis mosseae, Rhizoglomus irregulare, Septoglomus constrictus and Claroideoglomus lamellosum. The most abundant genera were represented by Glomus (29.7% of the sequences), Paraglomus (19.4%), Claroideoglomus (17.2%), Sclerocystis (16.1%) and Rhizoglomus (12.3%). Septoglomus, Diversispora and Funneliformis sequences corresponded to less than 4% of total sequences. Although the degree of root colonization was unaffected by treatments, ANOSIM analysis of PCR-DGGE clusters revealed significant differences in apple root AMF diversity between sites and agricultural managements. Species richness was significantly higher in organically managed orchards than in integrated ones. Our findings provide insights into important factors affecting native AMF communities of apple trees, which could be exploited in sustainable fruit production systems, where beneficial soil biota boost biogeochemical cycles, energy fluxes and crop productivity.