Salt stress is one of the most critical abiotic constraints on global agricultural productivity, negatively impacting plant growth, development, and yield potential. Watermelon, a moderately salt-sensitive crop, experiences substantial reductions in key growth parameters, including root and stem length, leaf count, and biomass production under salt stress. Understanding the genetic basis of salt tolerance is crucial for developing resilient cultivars. This study investigates the physiological and molecular responses of diverse watermelon genotypes to salt stress under controlled conditions, with a particular focus on identifying key molecular markers linked to stress tolerance. Under salt stress (8 dS m(-)1), the average root length of watermelon genotypes declined from 61.73 +/- 0.91 cm (control) to 55.85 +/- 0.73 cm, indicating an 8.16% reduction in root development. Chlorophyll a and b levels decreased by 17.1 and 13.6%, respectively, though specific genotypes (e.g., W7, W15, and W28) exhibited an increase in these parameters, suggesting potential tolerance mechanisms. Molecular marker analysis revealed that ISSR, SSR, and SRAP technologies effectively differentiate salt-tolerant and salt-sensitive genotypes. Notably, the ISSR-DBDACA7.540 band showed a strong association with photosynthetically active radiation (PAR) and malondialdehyde (MDA), achieving the highest regression coefficient (42.7%). These findings emphasize the varying salt stress responses among watermelon genotypes and highlight the critical role of molecular markers in evaluating and improving stress tolerance. The identified genetic resources can facilitate the selection of salt-tolerant genotypes and their incorporation into breeding programs, contributing to the development of more resilient watermelon varieties.