Genetic variations were detected in four rabbit genotypes; APRI line, New-Zealand White (NZW), Baladi Black (BB) and Gabali (GAB) breeds. Blood samples were taken from ten doe rabbits from APRI, NZW and BB in addition to seven does from GAB. Isozymes (esterase and peroxidase) and SDS-protein markers were used to detect the genetic variations within the four genotypes. RAPD-PCR analysis using six random arbitrary primers were employed to assess the genetic variations and phylogenetic relationships among the four genotypes. Results showed that there are a variation in both of protein and isozymes activity levels. Esterase profiles showed higher percentage of polymorphism (67.21%) than peroxidase (34.78%) and SDS-protein profiles (39.11%) within the studied genotypes. Overall mean of the genetic similarity within the studied genotypes based on all biochemical markers were 0.81 (APRI), 0.91 (NZW), 0.89 (BB) and 0.86 (GAB), which indicated high homogeneity within each genotype. The polymorphism percentage based on overall RAPD primers was 35.44% among the four genotypes, which suggest a kind of genetic diversity among the rabbit genotypes. From the dendrogram tree, both BB and GAB appeared to be closely related, while the APRI was the most different. The obtained results could have a great impact in rabbit breeding programs, such as selection or crossing programs.