Polychlorinated biphenyls (PCBs) have been used mainly as coolants and lubricants in transformers, capacitors, and other electrical equipments. Polybrominated diphenyl ethers (PBDEs) are still widely used as additive flame retardants. Both are among the most toxic environmental pollutants and reported as powerful endocrine disruptor. In Guanabara Bay previous studies have already detected PCBs, but the PBDE investigation is pioneer. A procedure for extracting simultaneously PCBs and PBDEs was developed and validated. Samples were collected, extracted, cleaned and analyzed by GC-MS. PCBs were the predominant pollutants, among them PCB-153 (2, 2’, 4, 4’, 5, 5’- hexachlorobiphenyl) proved to be the most disseminated one, with the highest content of 261 ng.g-1 dry weight (dw) in fish liver. PBDE occurrences were significantly lower, being the PBDE-47 (2, 2’, 4, 4’-tetrabromodiphenyl ether the most frequent, with the highest content of 46 ng.g-1 dry weight (dw) in fish tissue. In comparison to other ecosystems PCBs showed higher contents and PBDEs the lower ones.