Objective To study the genetic polymorphism of genomic DNA and genetic profile in a new guinea pig strain,and probe into the feasibility of RAPD-PCR method in genetic monitoring in guinea pig. Method The genomic DNA of Zmu-1:DHP strain and DHP guinea pig,as a compared strain, are amplified with the RAPD-PCR method. Results Two random primers with polymorphism were screened from 40 primers. No polymorphism occured in the amplified DNA product of Zmu-1:DHP strain, and the pattern of amplified product of Zmu-1:DHP strain was identical with most individuals of DHP strain. The amplified product of a small number of individuals in DHP strain demonstrated the polymorphism, and two characteristic DNA fragments were found in the strain.Conclusion The genetic homogeneity and the individual identity of Zmu-1:DHP strain is higher than DHP strain. There is a little difference between DNA sequences of the both strains. RAPD-PCR could be used in the identity of the strains and the monitoring of the genetic quality in guinea pig.