The effect of seafloor cold seeps on the biogeochemical cycling of mercury (Hg) remains enigmatic. Here we demonstrate substantial enrichments of mercury and methylmercury, along with the presence of microbes capable of metabolizing mercury in sediments of the Haima cold seep, South China Sea, by analyzing mercury and methylmercury concentrations, mercury isotopic composition analyses and metagenomic analyses of sediment cores. Compared to the reference area, the sediments in the upper sediment column of the active-seep area were 2.4 times enriched in Hg and 10.5 times in methylmercury. The slope of the capital delta ratio of mercury 199 to mercury 201 (Δ¹⁹⁹Hg/Δ²⁰¹Hg) with 1.23 ± 0.10 in the active-seep area indicate the occurrence of dark redox reactions. Genes related to mercury methylation (hgcA), demethylation (merB) and reduction (merA) were phylogenetically associated with several bacterial and archaeal linages. We roughly estimated an additional 2,835 Mg mercury and 9 Mg methylmercury are stored in cold seep globally. In summary, we propose that cold seeps globally function as a previously unrecognized sink for mercury and source for methylmercury in the deep ocean.