Genetic variation and phytochemical constituents of Dictyota dichotoma and Sargassum dentifolium, collected from Hurghada and Abu-Qir bay, were investigated. Results revealed an increase in the concentrations of carotenoids, sugars and DPPH% in the samples of both algal species collected from Hurghada as compared with those collected from Abu-Qir. In the samples collected from Hurghada, an increase in the concentrations of chlorophyll a, b and phenols was recorded in S. dentifolium; while a decrease in chlorophyll a, b only was observed in D. dichotoma. No significant difference was observed in phenol concentrations between D. dichotoma samples collected from the two studied localities. DNA was isolated and thirteen SCoT molecular markers were used to detect the genetic variation between samples from the two different localities. In D. dichotoma, the total average polymorphism is 56.68%. SCoT-1 exhibited the highest polymorphism (80%), while SCoT-28 recorded the lowest polymorphism (35.71%). In S. dentifolium, the total average polymorphism is 61.63%. SCoT-3 exhibited highest polymorphism (90%), while SCoT-13 exhibited the lowest polymorphism (0.09%).In addition, BSI factor shows a marked difference between the two studied algae that it was 0.87 % in D. dichotoma and 0.77 % in S. dentifolium. Variation in geographical location affects genetic variation and phytochemical composition of D. dichotoma and S. dentifolium. The difference in the responses of the two studied algae to the change of locality and environmental conditions may reflect differences in their gene expression. The efficiency of SCoT markers to discriminate between algal species collected from different localities has been confirmed.