Mercury (Hg) exchange between forests and the atmosphere plays an important role in global Hg cycling. The present estimate of global emission of Hg from natural source has large uncertainty partly due to the lack of chronical and valid field data, particularly for terrestrial surfaces in China, the most important contributor to global atmospheric Hg. In this study, micrometeorological method (MM) was used to continuously observe gaseous elemental mercury (GEM) fluxes over forest canopy at a clean site (Qianyanzhou, QYZ) and a contaminated site (Huitong, HT, near a large Hg mine) in subtropical south China for a full year from January to December in 2014. The GEM flux measurements over forest canopy in QYZ and HT showed net emission with annual average values of 6.67 and 1.21 ng m^−2 h^−1 respectively. Daily variations of GEM fluxes showed an increasing emission with the increasing air temperature and solar radiation in the daytime to a peak at 1:00 pm, and decreasing emission thereafter, even as a GEM sink or balance at night. High temperature and low air Hg concentration resulted in the high Hg emission in summer. Low temperature in winter and Hg absorption by plant in spring resulted in low Hg emission, or even adsorption in the two seasons. GEM fluxes were positively correlated with air temperature, soil temperature, wind speed, and solar radiation while negatively correlated with air humidity and atmospheric GEM concentration. The lower emission fluxes of GEM at the contaminated site (HT) when comparing with that in the clean site (QYZ), may result from a much higher adsorption fluxes at night in spite of a similar or higher emission fluxes during daytime. It testified that the higher atmospheric GEM concentration at HT restricted the forest GEM emission. Great attention should be paid on forest as a critical increasing Hg emission source with the decreasing atmospheric GEM concentration in polluted area because of the Hg emission abatement in the future.