Five-years crossing scheme involving the Spanish V-line (V) and Saudi Gabali (S) rabbits was practiced to produce new synthetic lines named Saudi-2 with structure of ((¾V¼S)2 ) 2 to be used as a maternal line. A total of 622 animals from Saudi-2 were used to perform both phenotypic and molecular analysis. From Operon Technologies, Alameda, 40 RAPD primers (Random Amplified Polymorphic DNA) were used to amplify to determine which primers can be used as genetic marker to differentiate between individuals of Saudi-2 and to study the association between these markers and daily gain rate traits and measures of respiration rates and body temperatures as indicator to heat stress resistance (respiration rates at 6 and 12 weeks of age, rectum temperature at 6 and 12 weeks of age, ear temperature at 6 and 12 weeks of age). DNA from grandsons of four sires was used to determine which primers out of 40 primers were amplified. Five markers (OPA121500, OPA191100, OPA201200, OPF09700 and OPF12900) were used later to search for the presence or absence of these markers in 618 grand progenies from the 5th generation of Saudi-2 line. Data of phenotypic values were analyzed using MTDFREML program to estimate the breeding values (EBV) of each animal for each studied trait. Linkage analyses between EBV and present or absent of markers bands were performed finally using multiple regression analysis. In general, results of molecular analyzes indicate that using RAPD markers was successfully linked to both body temperature and daily gain rate traits.