In this research, we genotyped 120 animal from Holstein breed and 100 animal from jersey breed using (GA)9C-ISSR and (AG)9C-ISSR markers. The genetic variability such as effective number, gene diversities, polymorphism percentage, number of polymorphic DNA fragments and Hardy-Weinberg equilibrium were calculated by POP Gene software. Number of polymorphic loci and polymorphism percentage based on marker were more in jersey breed than Holstein, demonstrating higher polymorphic percentage in Jersey breed. Analysis of Shannon Index and number actual effective also showed that genetic diversity is higher in Jersey breed. © 2010, INSInet Publication.