This pilot study documented the occurrence and levels of brominated flame retardants in the tissues of farmed and wild salmon in southern Chile. Samples of Coho salmon and rainbow trout were obtained from fish farms, rivers and lakes in the Patagonia in Aysen Region, Chile. The samples were analyzed by Gas Chromatography Negative Chemical Ionization Mass Spectrometry for the different polybrominated diphenyl ether (PBDE) congeners. Contaminants were observed in all the samples, and the congeners BDE 17, 28, 47 and 66 were observed in all both farmed and wild samples. The concentrations were higher in the farmed Coho salmon, presenting significant differences with wild salmon. The levels reached 182 pg/g wet weight (ww) vs. 120 ww. In the case of the rainbow trout, the concentrations were lower, although the congener profile was quite similar. The levels reached an average of 100 pg/g ww in the farmed fish versus 110 pg/g ww in wild fish, and no significant difference was observed between the species. In both species, the congener with the highest concentration was BDE 47. Based on this information, the BDE flow was estimated for commerce, which is a form of pollutant transport not usually considered in POP pollution studies. A preliminary estimation indicated that the quantity of PBDEs mobilized by commerce was in the order of kg, and in the case of Chile might reach almost 1 kg.