Both total mercury (THg) and methylmercury (MeHg) levels in fish collected from South China Sea (SCS) were studied to understand Hg pollution in Chinese tropical marine ecosystems. The average THg concentrations in fish species ranged from 39.6 μg/kg for rabbitfish (Siganus fuscessens) to 417 μg/kg for thornfish (Terapon jarbua), while those of MeHg varied from 13 μg/kg (rabbitfish) to 176 μg/kg (thornfish). The median values of MeHg/THg ratios in different fish species ranged from 36 to 85%. Significant inter-species differences of THg and MeHg in fish were observed due to feeding habits and fish sizes. Overall, carnivorous fish had higher levels of THg, MeHg and MeHg/THg ratios than omnivorous and herbivorous fish. High Hg levels in fish of the SCS were probably related to Hg input from atmospheric deposition and anthropogenic activities.