Most seeds prefer temperature below 30 C° for germination, but since temperature control in the field is not possible, this study aims  to increase Lepidium sativumplant tolerance to heat stress by pretreatment with ultrasonic waves. Results revealed that 25 C° was the ideal temperature for garden cress seed germination. Heat stress at 30, 35, and 40 C° caused a progressive decline in the germination percentage and all growth criteria, and at 40 C° no seed germination was observed even after pretreatment with ultrasonic waves. Furthermore, exposure of seeds to ultrasonic vibrations, especially for 20 minutes at temperatures up to 35 C°, resulted in a significant increase in germination percentage up to 96% compared to the corresponding control percent 92%, all seedling growth parameters and mineral ion contents at all tested temperatures, in addition to decrease in stress markers. Soluble sugars and proteins also increased, recording 131.64 and 20.65 mg/g dry matter respectively compared to corresponding control. The dendrogram and Principal Component Analysis (PCA) plot were designed based on morphological and physiological parameters and showed three groups of variable treatments. A molecular marker RAPD-PCR was applied to estimate the genetic variance resulting from ultrasonic exposure time and heat stress on Lepidium sativum. The total polymorphism percentage was 48.61%. In conclusion, ultrasonic waves up to 20 minutes exposure time can be used as seed pretreatment before sowing to help in adaptation to high temperatures.