This work aimed at studying the genetic diversity among different rabbit genotypes reared in Egypt by two different molecular markers (start codon targeted, SCoT, and inter-simple sequence repeat, ISSR) to improve breeding strategies. Five different groups of rabbits were used Gabali (Gab), New Zealand white (NZW), Californian (Cal), Rex, and Papillon (Pap). DNA was extracted and analyzed using SCoT and ISSR-PCR, and the obtained fragments were analyzed. Six SCoT primers scored 60 bands with 78.33% polymorphism; primer SCoT 6 was the most polymorphic marker with 92.31% polymorphism, while SCoT 5 was the lowest with 60 %. A dendrogram based on SCoT-PCR revealed that the Rex breed was the most genetically different. Seven ISSR primers gained 56 bands in total with 49.762% polymorphism. ISSR 4 was the most polymorphic primer that detected 75%of polymorphism, while ISSR 6 was not able to detect any polymorphism. It was suggested that the SCoT markers may be more effective than ISSR for differentiating and identifying the genetic variations within investigated breeds. Also, the usage of molecular markers of SCoT and ISSR may be more proper for calculating genetic diversity and common ancestry among tested rabbit breeds. Furthermore, evaluating genetic variability is important for enhancing existing breeds’ adaptation to ecological alterations and crucial for preservation or breeding purposes.