East Asia is one of the largest source regions that release mercury into the atmosphere. Although extensive studies have been devoted to estimating the anthropogenic mercury emission, little is known about mercury emission from natural sources in the region. In this study, we adapt the algorithms developed previously, coupled with detailed GIS data and satellite LAI products, to estimate mercury emission from natural sources including vegetation, soil, and water surfaces in an East Asian domain containing 164 × 97 grid cells at a spatial resolution of 36 km. Seasonal simulations were performed to project the annual emission quantity. The simulated emission shows strong diurnal and seasonal variations due to meteorology and vegetation coverage. The annual emission in the form of gaseous elemental mercury (GEM) from the domain in 2001 is estimated to be 834 Mg, with 462 Mg contributed from China. The estimated GEM emission is comparable to the reported anthropogenic emission of 575 ± 261 Mg (56% GEM, 32% reactive gaseous mercury, 12% particulate mercury; Wu, Y., Wang, S., Streets, D.G., Hao, J., Chan, M., Jiang, J., 2006. Trends in anthropogenic mercury emissions in China from 1995 to 2003. Environmental Science & Technology 40, 5312–5318) in China for the year 2001, and dominates the anthropogenic emission during the warm season. Combining the anthropogenic and natural emission estimates, the total mercury emission from China is 776–1298 Mg, with GEM being in the range of 660–1000 Mg. The latter is similar to the GEM emission quantity inferred from aircraft measurement (765 Mg; Friedli, H.R., Radke, L.F., Prescott, R., Li, P., Woo, J.-H., Carmichael, G.R., 2004. Mercury in the atmosphere around Japan, Korea and China as observed during the 2001 ACE Asia field campaign: measurements, distributions, sources, and implications. Journal of Geophysical Research 109, D19 S25) and modeling estimate (1140 Mg; Pan, L., Chai, T., Carmichael, G.R., Tang, Y., Streets, G.G., Woo, J.-H., Friedli, H.R., Radke, L.F., 2007a. Top-down estimate of mercury emissions in China using four-dimensional variational data assimilation. Atmospheric Environment 41, 2804–2819) in China for the year 2001. The estimated natural emission helps explain the gap between the anthropogenic emission estimates based on activity data (e.g., Pacyna, J.M., Pacyna, E., Steenhuisen, F., Wilson, S., 2006. Global anthropogenic mercury emission inventory for 2000. Atmospheric Environment 40, 4048–4063; Wu, Y., Wang, S., Streets, D.G., Hao, J., Chan, M., Jiang, J., 2006. Trends in anthropogenic mercury emissions in China from 1995 to 2003. Environmental Science & Technology 40, 5312–5318) and the emission inferred from field observations (e.g., Jaffe, D., Prestbo, E., Swartzendruber, P., Weiss-Penzias, P., Kato, S., Takami, A., Hatakeyama, S., Kajii, Y., 2005. Export of atmospheric mercury from Asia. Atmospheric Environment 39, 3029–3038; Weiss-Penzias, P., Jaffe, D., Swartzendruber, P., Hafner, W., Chand, D., Prestbo, E., 2007. Quantifying Asian and biomass burning sources of mercury using the Hg/CO ratio in pollution plumes observed at the Mount Bachelor observatory. Atmospheric Environment 41, 4366–4379) in the region.