The Yarlung Zangbo River is the highest river in the world. It flows from west to east through the southern part of Tibet. The mercury (Hg) speciation and distribution in surface waters and soils near the bank of the Yarlung Zangbo River and its two tributaries, the Lhasa and Niyang Rivers, were investigated in June 2007. Simultaneously, major water quality parameters were also measured at the same stations. Total Hg (THg) and total methylmercury (TMeHg) concentrations in surface waters of the Yarlung Zangbo River ranged from 1.46 to 4.99 ng/L and from 0.06 to 0.29 ng/L, respectively, representing the background levels in river systems of the Tibetan Plateau. Particulate Hg (PHg) accounted for 69% of the THg, and the two Hg species had a significant relationship (r=0.990, P<0.01). Approximately 61% of the spatial distribution of THg was controlled by the concentrations of total suspended particles (TSP). Reactive Hg (RHg) concentrations ranged from 0.10 to 0.36 ng/L, and this fraction may play a weak role in terms of the transport and fate of Hg in surface waters. Dissolved methylmercury (DMeHg) constituted 71% of the TMeHg and was significantly correlated with TMeHg (r=0.746, P<0.01). The spatial distribution of TMeHg is not strongly affected by environmental factors such as THg, RHg, temperature, pH, dissolved organic carbon (DOC), and TSP. In addition, the inflow of both the Lhasa and Niyang Rivers probably influences the concentrations of THg in surface waters of the mainstream, but such an effect is not obvious for TMeHg.