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The genetic variation in two indigenous Pakistani goat breeds (Damani and Nachi) was studied with 9 microsatellite markers in order to determine the genetic diversity between them. A total number of 50 non relative individuals of Damani (25) and Nachi (25) were sampled to explore genetic polymorphisms and relationship between these two important goat breeds. Result revealed considerable level of genetic diversity in both breeds and a total number of 53 alleles were identified with mean of 3.2 in Damani and 4.6 in Nachi. The genetic diversity in both breeds ranged from 0.51(Nachi) to 0.73 (Damani). High level of genetic differentiation (FST = 0.20) and low level of gene flow (Nm=0.95) found could be due to their divergent or expanded geographical locations. Heterozygote across two populations (FIT) was found to be 0.15. The mean Polymorphic Information Content (PIC) was 0.70 ranging from 0.54 (MAF33) to 0.83 (ILSTS011), revealed the high level of polymorphism for studied microsatellite markers set in this study. The measures of genetic variation revealed that there is good scope for effective improvement, conservation and designing national breeding policies for goat breeds in future.