PurposeDrought and waterlogging are one of the most severe abiotic stresses towards plant growth and development. The experiment was implemented in the Isfahan University of Technology's research greenhouse to examine the effect of melatonin foliar spraying in hot pepper plants under waterlogging and drought stresses. MethodsThis factorial experiment was performed as a complete randomized design (CRD) in triplicate. The treatments included controls, waterlogging, drought stress, and melatonin foliar spraying at 0 and 500 µM concentrations. ResultsThe results demonstrated that the foliar melatonin spraying was more advantageous under drought and waterlogging stress conditions via increasing ammonium content, NR (nitrate reductase activity), chlorophyll content, proline, protein, transpiration, shoot length, root water content, amino acid alterations, and PIP gene expression. ConclusionsMelatonin influenced the hot pepper's growth by affecting enzyme activity NR hormonal changes (ABA), amino acid changes, and PIP gene expression.