Analytical method using mass spectrometric techniques was applied for the determination of polybrominated diphenyl ethers (PBDEs) in freshwater fishes. Fish samples collected from Nanyang River contaminated by the recycling electron-wastes (e-wastes) materials were prepared by using Soxhlet extraction and multiple-step column chromatographic clean-up. PBDEs were determined by gas chromatography (GC) coupled with ion trap mass spectrometry (for mono- to hepta-BDEs) and quadrupole mass spectrometry (for BDE-209). The method performance was evaluated with the recovery of (13)C-labeled internal standards and with the analysis of certified reference biota. The obtained recoveries ranged from 75 to 125% with a relative standard deviation of lower than 10% for 16 PBDE congeners. The total PBDE (SigmaPBDE) concentrations in fishes showed the following trend: grass carp<mud carp<crucian carp<silver carp<carp. SigmaPBDE concentrations in the abdomen, back and tail muscles of carp ranged from 766, 458 and 530 ng/g w.w., and 53, 52, 45 ng/g w.w. in grass carp, respectively. The SigmaPBDE concentrations in abdomen muscles were no significantly higher than in back and tail muscles in carp, crucian carp, grass carp and mud carp. PBDE congener concentrations in muscles correlated well with their lipid content. BDE-47 and BDE-28 were the most abundant congeners followed by BDE-17, BDE-15, BDE-66, BDE-154 and BDE-153 in fishes collected from Guiyu.