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There are differences in the response of long-term mercury (Hg) deposition to climate change, so it is necessary to clarify the influencing factors of Hg deposition in different locations. The Dahu and Daping Swamps are located in the eastern and western parts of the Nanling Mountains in South China, respectively. They are asynchronous variations of Hg deposition reflected by the two swamps since the last deglaciation. Based on the comprehensive comparative analysis of physical, chemical, and biological proxies, it is indicated that Hg deposition changes in the Dahu and Daping mainly record the changes in Hg content in the catchment input from organic matter. The differences in organic matter sources, core surrounding environment, Hg sources and atmospheric sedimentation contribution are reasons associated with the catchment environment for the observed differences in swamp Hg deposition and the response to climate. In cold/dry periods, Hg adsorption by terrestrial organic matter in Dahu Swamp were more significant, while in warm/humid periods, Hg adsorption by endogenous organic matter in Daping Swamp and wet deposition of nearby Hg sources, were the main climate-related processes for their asynchronous response. In addition, Dahu and Daping Swamps show similarities and differences in their Hg deposition variations. In both swamps, multi-millennial (∼1000−2200yr) and multi-centennial cycles (∼300–500yr) were observed and may be related to the harmonic period of the Earth's precession cycle and the solar activity cycle. This study helps to understand the differences in response between sedimentary Hg and climate, and to understand the regional and global proxies used to record climate and environmental changes. • Hg deposition investigated in two swamps in the Nanling Mountains in South China. • Hg deposition in subtropical swamps responds to climate changes since the Last Deglaciation. • Changes in Hg deposition are asynchronous in the two swamps. • Low latitude climate processes affect EASM strength and Hg deposition in South China. • Millennial and centennial scale cycles in Hg deposition are also recorded. [ABSTRACT FROM AUTHOR]