Melatonin (MEL) and salicylic acid (SA), synthesised from the same precursor molecule chorismic acid, are known as molecules that support plants to develop tolerance against stress factors. In this study, antagonistic/synergistic effects of MEL and SA were determined on the basis of germination, plant growth and biochemical changes using onion with relatively small genome under drought stress. Germination and development of bulbs exposed to drought at -0.60 MPa were suppressed. Only MEL treatments (100, 200, 300 mM) had a promoting effect, while interestingly SA (10, 20, 30 mM) and MEL/SA combinations suppressed germination and vegetative growth. Even root formation was completely inhibited in the presence of SA. 200 mM MEL increased the germination rate up to 88 % under drought conditions. In addition, the number of leaves, which is an important yield parameter for onion, increased to 9.3 in 200 mM MEL, even exceeding the control treatment. Proteinogenic amino acids, water soluble vitamins and mineral content increased as a result of MEL applications. On the other hand, there was no increase in organic acid content as expected in onion, which is an alkaline sensitive species. SA and SA/MEL suppressed the growth by causing protein degradation. It was determined that SA doses used in the study had antagonistic effect with MEL under drought stress and reversed the ameliorative effect of MEL under drought conditions. For this reason, it is recommended that MEL/SA combinations should be used more carefully depending on plant species and dose.