The present study evaluates the genetic diversity of black francolin (Francolinus francolinus asiae) in Uttarakhand on the basis of microsatellite loci. For this purpose, we examined five populations from three geographical zones of Uttarakhand, Western Himalaya. Microsatellite markers were polymorphic with number of alleles per locus ranging from 4-21, effective number of alleles per locus from 1.34 to 4.93, the Polymorphic Information Content (PIC) value ranged from 0.22 to 0.85. The averaged observed heterozygosity across all loci were Ho=0.320.12 and averaged expected heterozygosity He=0.510.06 respectively. The genetic structure showed that there were two genetically distinct clusters. The Lesser Himalayan and Himalayan foothill population forming a single cluster and population of Tarai region forming another cluster. The pairwise FST results showed a sizeable genetic difference between the population of higher and lower altitude. The AMOVA showed that higher levels of variation were observed among individual within populations (64.36%) and lower differentiation observed among populations (2.99%). Overall the populations of black francolin were genetically variable with high adaptive potential in Uttarakhand, Western Himalaya.