Abstract: Genetic diversity of 10 microsatellite locis were analyzed in Chai chicken breeds. Allele frequency, effective number of alleles, heterozygosity, Polymorphism Information Content (PIC), F-statistics, migration rate were calculated. The results showed that the average observed Heterozygosity (Ho) and PIC amongst populations ranged from 0.5353-0.5614 and 0.5108-0.5199, respectively. The genetic diversity was very rich and was of high selective potency. To analyze population structure, pairwise Fst coefficients explained only 8.4% variability from the breed differences, the remaining variability stems from individual differences. Gene flow of microsatellite loci was 2.7794 indicate no significant genetic differentiation among populations.