The study was planned to compare six pure rabbit breeds (Gabali, Chinchilla, V-line – Bouscat, New Zealand White and California) using random amplified polymorphic (RAPD) molecular markers and phenotypic characteristics. A total of 115 amplified bands were scored out of them 98 were polymorphic. The percentage of polymorphism (%P) ranged from 42.86% to 100.00%. The cluster analysis revealed similarity coefficient values ranged from 0.31 (Gabali and California) to 0.66 (Bouscat and New Zealand). A cluster analysis realized using percentage of similarity method for phenotypic data, revealed similarity coefficient values ranged from 77.74 (California and Gabali) to 96.37 (Bouscat and V Line). Results of single marker analysis showed seven, five and four RAPD markers related to body weight, body tall and mortality rate (MR) traits, respectively. The marker OPA-13200bp was significantly associated with litter's weight at weaning (LWW) (r=0.010, p=0.041). The associated markers each explained a maximum regression of 69.00 (LWW) to 93.00% (MR) of the total available variation for individual associated traits. The phenotypic data showed that New Zealand rabbits had the highest body weight and the body tall compared with the other pure breeds. The highest pre-weaning mortality rate was for Bouscat rabbits compared to other pure breeds. In the same direction, the highest LWW was for California rabbits.