Salinity and drought are two of the most important environmental factors that cause reduction in plant growth, development and productivity worldwide. In the present study, we have investigated the effect of citrulline on drought and salt tolerance in watermelon genotypes. Seeds were germinated in plastic pots containing vermiculite. Plants with three true leaves were subjected to drought and salt stress. Stress responses of the watermelon genotypes were evaluated in early plant development stages. Genotypes were classified according to their citrulline level. Watermelon genotypes with tolerance to salt, KAR-152, KAR-278, KAR-306 and KAR-338, were induced to accumulate citrulline. On the other hand, genotypes with drought tolerance KAR-98, KAR-234, KAR-278, KAR-300, KAR-306 and KAR-374 accumulated higher levels of citrulline than sensitive genotypes. The result of the study, evaluating citrulline as a biochemical marker for salt and drought tolerance of watermelon genotypes is discussed.