Synthetic musks are ubiquitous pollutants in aquatic environments. As hydrophobic chemicals, they can accumulate in terrestrial and aquatic organisms. Investigations into the bioaccumulation of these chemicals in aquatic ecosystem have, however, been limited, and previous results were inconsistent among species and ecosystem. Studies on this topic have been carried out in European countries, the USA, and Japan, but very few are known of the situation in China. The aim of this study was to investigate contaminant levels of musks in fish from Taihu Lake, the second largest freshwater lake in China, as well as bioaccumulation and biomagnification of the pollutants in the freshwater food chain. Five polycyclic musks and two nitro musks were determined in 24 fish species and nine surface sediment samples from Taihu Lake. HHCB (1,3,4,6,7,8-hexahydro-4,6,6,7,8,8-hexamethylcyclopenta[γ]-2-benzopyran) and AHTN (7-acetyl-1,1,3,4,4,6-hexamethyl-1,2,3,4-tetrahydronaphthalene) were the predominant contaminants in the fish samples, with concentrations ranging from below the limit of detection (LOD) to 52.9 and from <LOD to 7.5 ng/g lipid weight, respectively. Other contaminants were at low detection frequencies. The results indicated low concentrations of musks yet widespread occurrence of these contaminants in fish from Taihu Lake. Species-specific and lipid-related bioaccumulation characteristics were suggested, but no significant region-specific differences were observed. Normalized biota-sediment accumulation factors for HHCB and AHTN were noted to increase with trophic levels in fish. Trophic magnification factors were estimated at 1.12 for HHCB and 0.74 for AHTN. A biomagnification for HHCB, and probably biodilution for AHTN, in the freshwater food chain are indicated, when trophic magnification factors were concerned. However, the correlations between logarithmic concentrations of the chemicals and trophic levels were not statistically significant. Further study using long food chains in this lake is still needed.