Salinity stress threatens growth and productivity of important crops such as barley and wheat. Plant hormones are important regulators of plant growth, development and response to abiotic stress. In this study, changes in endogenous serotonin and melatonin in barley and wheat under 150 mM salt (NaCl) were measured along with morphological, physiological and biochemical stress markers. Root biomass decreased by 38.40 and 51.04 %, reserve mobilisation decreased by 49.56 % and 64.31 % and proline increased by 34.29 and 38.26 % of the control in salinity treated barley and wheat, respectively. The activity of superoxide dismutase (SOD) increased in salinity treated barley and wheat plants by 372.71 and 312.60 U/g FW compared to the control, respectively. Both serotonin and melatonin increased in saline treated wheat plants by 45.90 and 55.32 % of the control. In barley, serotonin decreased by 65.75 % of the control and melatonin was not affected by salinity stress. In wheat, the increase in serotonin and melatonin was accompanied by increased proline content, decreased reserve mobilisation and increased antioxidant activity. In contrast, serotonin was decreased in barley, which was accompanied by increased activity of antioxidant enzyme and enhanced reserve mobilisation. The findings of this study could be utilised in screening different barley and wheat cultivars for the correlation between changes in melatonin and serotonin and enhanced salinity tolerance at the germination stage. This might help in identifying cultivars with improved germination under salinity stress.