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Sucrose and proline metabolisms are often associated with drought tolerance of plants. This study was conducted to investigate the effects of two arbuscular mycorrhizal fungi (AMF) species (Funneliformis mosseae and Paraglomus occultum) on root biomass, lateral root number, root sucrose and proline metabolisms in trifoliate orange (Poncirus trifoliata) seedlings under well-watered (WW) or drought stress (DS). All the AMF treatments significantly increased root dry weight, taproot length, and the number of lateral roots in 1st, 2nd, and 3rd class under WW and DS. Mycorrhizal seedlings conferred considerably higher fructose and glucose concentrations but lower sucrose accumulation, regardless of soil water status. Under DS, F. mosseae treatment significantly increased root sucrose synthase (SS, degradative direction) and sucrose phosphate synthase (SPS) activity but deceased root acid invertase (AI) and neutral invertase (NI) activity, and P. occultum inoculation markedly increased root AI, NI, SS, and SPS activities. AMF treatments led to a lower proline accumulation in roots, in company with lower activities of Δ1-pyrroline-5-carboxylate synthetase (P5CS), δ-ornithine aminotransferase (OAT), Δ1-pyrroline-5-carboxylate reductase (P5CR), and proline dehydrogenase (ProDH) in roots. It appears that the AM symbiosis induced greater root development and sucrose and proline metabolisms to adapt DS.