The brominated flame retardant decabromodior phenyl ethane (DBDPE), an alternative to decabrominated diphenyl ether (BDE209), has become a widespread environmental contaminant, but its possible toxic effects to wildlife remain unknown. Using zebrafish as a model, we investigated the bioconcentration and impact of DBDPE on thyroid endocrine function after water-borne exposure, compared to BDE209. Zebrafish embryos were exposed to DBDPE or BDE209 (0, 3, 10, 30, 100, 300 nM) for 6 or 14 days. Chemical analysis revealed that DBDPE and BDE209 were bioconcentrated in zebrafish larvae, with similar magnitudes of accumulated concentrations. Based on screened by chromatograms, at least seven unknown compounds were observed in DBDPE-treated larvae, indicating biotransformation of the chemical. Significant increases in whole body content of triiodothyronine (T3) and thyroxine (T4) were detected in DBDPE-treated larvae, but decreased in BDE209-treated groups. Alterations in gene transcription along the related hypothalamic-pituitary-thyroid (HPT) axis were observed. Furthermore, the binding and transport protein transthyretin (TTR) was significantly increased in DBDPE exposure groups. Histological examination and stereological analysis showed no obvious pathological changes in the thyroid gland. The present study demonstrates for the first time the bioavailability, biotransformation and thyroid endocrine disruption associated with DBDPE exposure in fish. Further studies are warranted to identify the metabolites of DBDPE and to define its environmental risks to aquatic organisms.