The present investigation aimed to analyze PBDE and PCB contamination in mussels (Perna perna) and two commercially important fish species, croaker (Micropogonias furnieri) and mullet (Mugil liza), in the Guanabara Bay, the most important Brazilian estuary, by gas chromatography coupled to mass spectrometry, in order to further knowledge regarding these compounds in the southern hemisphere. This is also the first report of PBDE in this mussel species in the Guanabara Bay. Fish were captured in September (dry season, winter) and March (wet season, summer) 2007 and September 2008. Mussels were collected in August (dry season, winter) 2006, in February (wet season, summer) 2007, and in August 2007 (winter). The results show that all samples showed higher PCB contamination when compared to other ecosystems around the world. On the other hand, PBDEs presented lower concentrations in 41 % of the samples. Croakers presented the highest PCB and PBDE levels, with mullet showing intermediary values and mussels, the lowest.