Abstract Melatonin is a pleiotropic signaling molecule, which besides being involved in various growth and developmental processes and mediates environmental stress responses, but whether and how endogenous melatonin involved in salt response was still unknown. Here, we elucidated the involvement of endogenous melatonin in salt response by the investigation on the loss-of-function mutants of melatonin biosynthesis genes SNAT1 and SNAT2 . We found the double mutant snat1snat2 with attenuated melatonin synthesis exhibited salt sensitivity, manifesting by unhealthy plant growth, ion imbalance and ROS accumulation under salt stress. Transcriptomic profiles of snat1snat2 showed the expression of large number of salt-responsive genes were affected by SNAT defect, and these genes were closely related to the synthesis of auxin and several signaling pathways. In addition, the salt sensitive growth phenotype of snat1snat2 was alleviated by applying exogenous auxin. Our results show that endogenous melatonin is required for plant salt tolerance, which is correlated with its large activity in mediating auxin signaling.