Drought-tolerant plants have become a convenient model to study the mechanisms underlying drought tolerance to improve the susceptible domesticated relatives. Various studies have shown that wild watermelon possess superior qualities that aid its survival in harsh environmental conditions. One of the key mechanisms that aids the tolerance of the crop has been noted as its timely stomatal regulation. In this study, the physiological, morphological and molecular stomatal responses of a drought-tolerant (wild watermelon) and four other watermelons genotypes were evaluated under drought stress. The watermelon plants were grown under water deficit (complete withholding of watering) and non-stress treatment. The highest SPAD values were recorded in wild and cooking (50 ± 3) watermelon genotypes and Crimson sweet (27 ± 0.37) had the lowest SPAD values showing the ability of the tolerant genotypes to maintain their system during drought stress. Fluorescence parameters also gave an important clue into the tolerant genotypes with cooking and wild watermelon under drought stress while the domesticated genotypes showed slow response to fluorescence parameters, something that might lead to damage to photosynthesis apparatus. Stomatal opening during drought showed that the wild watermelon limited its opening with the progress of drought as at day 9 it had the lowest opening of 23.1 ± 1.2 µm as compared to other genotypes and most importantly upon re-watering it showed rapid recovery than all the genotypes. And these was also expressed in mRNA quantification of stomatal aperture TFs where wild watermelon recorded 8 fold increase on stomatal closure CLROC3 TFs. And all these mechanisms have been attributed to the tolerance mechanisms of the drought tolerant watermelon genotypes.