By determining mercury concentrations in mercury ore and smelting slag samples, we used a mass balance method to calculate mercury emission factors and annual mercury emission from the indigenous method of mercury smelting in Wuchuan mercury mining areas, Guizhou Province. The mercury emission factors of the indigenous method ranged from 6.9% to 32.1% with the recovery from 78.4% to 93.6% and the annual mercury emission was up to 3.7-9.6 tons. The results highlighted that the indigenous mercury smelting was one of the most important anthropogenic atmospheric mercury emission sources in this region.