A total of 149 goats from two Thai indigenous breeds (northern and southern), two exotic breeds (Anglo-Nubian and Boer), and an original Thai meat goat population were genotyped with 26 microsatellite markers. The average number of alleles observed was 9.3. The observed and expected heterozygosity (HO and HE) for the population ranged 0.52-0.71 and 0.60-0.66, respectively. The HO and HE of southern Thai indigenous goats (0.52 and 0.62, respectively) were lower than those of the northern Thai indigenous goats (0.67 and 0.63, respectively). Analysis of Nei's genetic distances and Bayesian-modelbased clustering grouped the two indigenous goat breeds together and separated them from the two exotic breeds. A combined dendrogram obtained by adding Asian indigenous goat populations showed that the northern Thai indigenous goats are closest to Bangladesh Black Bengal, the dendogram of which was located in the major southeastern Asian indigenous goat clade with southern Thai indigenous goats. The original population (a hybrid with 50% Boer, 25% Anglo-Nubian, and 25% southern Thai indigenous ancestry) was located close to Boer and Anglo-Nubian; it formed a separate clade from that of the Thai indigenous goats. Genetic characterization of these genetic resources provides essential information for conservation and breeding programs.