To examine the potential roles of melatonin in Cd uptake, accumulation and detoxification in Malus plants, we exposed two different apple rootstocks varying greatly in Cd uptake and accumulation to either 0 or 30 μM Cd together with 0 or 100 μM melatonin. Cd stress stimulated endogenous melatonin production to a greater extent in the Cd-tolerant M. baccata than in the Cd-susceptible M. micromalus ‘qingzhoulinqin’. Melatonin application attenuated Cd-induced reductions in growth, photosynthesis, and enzyme activity, as well as ROS and MDA accumulation. Melatonin treatment more effectively restored photosynthesis, photosynthetic pigments, and biomass in Cd-challenged M. micromalus ‘qingzhoulinqin’ than in Cd-stressed M. baccata . Exogenous melatonin lowered root Cd2+ uptake, reduced leaf Cd accumulation, decreased Cd translocation factors ( T f s), and increased root, stem, and leaf melatonin contents in both Cd-exposed rootstocks. Melatonin application increased both antioxidant concentrations and enzyme activities to scavenge Cd-induced ROS. Exogenous melatonin treatment altered the mRNA levels of several genes regulating Cd uptake, transport, and detoxification including HA7 , NRAMP1 , NRAMP3 , HMA4 , PCR2 , NAS1 , MT2 , ABCC1, and MHX . Taken together, these results suggest that exogenous melatonin reduced aerial parts Cd accumulation and mitigated Cd toxicity in Malus plants, probably due to the melatonin-mediated Cd allocation in tissues, and induction of antioxidant defense system and transcriptionally regulated key genes involved in detoxification.