Two ornithogenic sediment cores, which have a time span of 1000 years and are influenced by red-footed booby (Sula sula), were collected from Dongdao Islands, South China Sea. The determined mercury concentrations of the two cores show similar and substantial fluctuations during the past millennium, and the fluctuations are most likely caused by the changes in mercury level of the ocean environment and in anthropogenic Hg emission. For the past 500 years, the mercury concentration in the red-footed booby excrement has a striking association with global anthropogenic mercury emission. The mercury concentration increased rapidly after AD 1600 in corresponding to beginning of the unparalleled gold and silver mining in South Central America that left a large volume of anthropogenic mercury pollution. Since the Industrial Revolution, the mercury level has increased at a fast pace, very likely caused by modern coal combustion, chlor-alkali and oil refining industries. The comparison of mercury profiles from different places on earth suggested that anthropogenic mercury pollution after the Industrial Revolution is more severe in Northern Hemisphere than in Antarctica.