Situated in the south edge of the Tibetan Plateau, the Himalayas is expected to receive direct anthropogenic Hg perturbations from South Asia, yet the measurements of atmospheric Hg deposition in the Himalayan region remain scarce. Here we report wet Hg deposition measured in the Yarlung Tsangpo Grand Canyon of the Eastern Himalayas, which is the deepest and longest canyon on earth. The precipitation Hg concentration (56.3 ng L−1) and wet Hg deposition flux (84.7 μg m−2 yr−1) from the Motuo station were observed among the highest ever reported for the Tibetan Plateau. Together with analysis of principal component suggesting Hg was mainly clustered with anthropogenic ions and backward trajectories indicating 88.8% of air masses came from South Asia, our results show that transboudary pollution influences from South Asia could be largely responsible for the unexpectedly high levels of wet Hg deposition. Moreover, the wet Hg flux measurements (84.7 μg m−2 yr−1) are found an order of magnitude (∼13 times) higher than the GEOS-Chem estimates (6.8 μg m−2 yr−1), most likely due to the underestimation of transboundary Hg pollution influence by this model. Our study has important implications for better understanding Hg dynamics and verifying atmospheric Hg models in the Tibetan Plateau and Himalayas region.