The current study aiming at Goat populations in Ha Giang based on microsatellite markers was undertaken. A total of 301 goats from 5 districts in Ha Giang were genotyped for 20 microsatellite markers recommended by FAO. Seventeen of twenty microsatellite markers used in this analysis had four or more alleles with mean number of allele/locus were 7.12. The mean expected heterozygote and the mean observed heterozygote for all populations ranged from 0.22 (SRCRSP7 and INRA063) to 0.63 (OARFCB20) and 0.28 (SRCRSP7) to 0.76 (OARAE54), respectively. The mean Fis of 0.293 showed high inbreeding in Ha Giang goat populations. The mean Fst (0.047) demonstrated that about 95.3% of the total genetic variation was due to the genetic differentiation within each population. A phylogenetic tree based on the Nei (1972) standard genetic distance displayed 3 genetic groups: Dong Van, Meo Vac and Quan Ba, Hoang Su Phi and Xin Man group in the population. The mean Fis values of phenotypic groups (hornless, long-hair and prolific group) ranged from 0.275 to 0.331. Genetic variation (Fst values) between these groups was very small. Conservation of Ha Giang goat populations should be established according to phenotypic characteristics.