BDE-209 is the most commonly used commercial polybrominated diphenyl ether, and is of particular concern due to its accumulation and debromination to more toxic congeners in aquatic organisms. In this study, Japanese medaka were continuously exposed to BDE-209 with the exposure concentrations ranging from 1 to 1000 ng/L for 15, 30 and 60 days in a flowing-through exposure device. The results showed that BDE-209 could be accumulated in fish muscle at environmental relevant concentrations and its concentration in the muscle increased with the increase of exposure time and reached to a steady state. Toxicokinetic data showed that the dose-dependent half-life of BDE-209 in the muscle of medaka ranged from 16.5 to 19.4 days. Low brominated congeners could be detected, where tri- to hexa-BDEs were predominant congeners with up to 46% to 93% of total PBDEs and lower brominated BDEs may have slower elimination rates. Concentration level of BDE-155 ranged from several ng/g wet weight (ww) to a maximum of 178 ng/g ww. BDE-154 and BDE-153 as intermediates in fish under continuous exposure were negligible. By comparing with previous work, fish may have a different bioaccumulation capacity and metabolic pattern from other species, either because of species difference or the manner of exposures.