Fenugreek is a globally important legume that is widely cultivated for its therapeutic benefits in most parts of the world. Seeds on the other hand have a poor germination and growth rate when exposed to salinity. The effect of ultrasonic exposure period on germination and early seedling behaviors of fenugreek seeds under salt stress was investigated in a laboratory experiment. During germination and early seedling stages, all tests were conducted at 40 kHz in a water bath ultrasonic device with two durations (10 and 20 min) under salinity stress using different concentrations of NaCl (0, 1000, 3000, and 5000 mg/l). The results revealed a substantial decrease in germination percentage, all growth criteria, with increasing NaCl concentration and a significant increase in biomass produced by the Fenugreek (total soluble protein, total soluble carbohydrate, and proline), all of which are thought to be mechanisms for salinity resistance. Ultrasonication of fenugreek seeds for 10 and 20 min has a significant impact on seed germination, early seedling development and biochemical constituents under normal and stress conditions. The genetic stability of fenugreek DNA content was affected by these different treatments. This variation was estimated by RAPD-PCR molecular marker, and resulted in a total polymorphism percentage of 49.72% from all the primers. All these different treatments caused variation in the physiological responses and DNA content. This variation enhanced with more ultrasonic and salt treatments. Hence, these stresses can be used for enhancing the variable metabolic processes in fenugreek plant and stimulate its medicinal properties.