Although polychlorinated biphenyls (PCBs) and polybrominated diphenyl ether (PBDE) flame retardants are important organic contaminants in the tissues of marine mammals, including those species from the Arctic, there is exceedingly little direct evidence on congener-specific biotransformation. We determined and compared the in vitro metabolism of environmentally relevant PCB (4,4'-di-CB15, 2,3',5-tri-CB26, 2,4,5-tri-CB31, 2,2',5,5'-tetra-CB52, 3,3',4,4'-tetra-CB77, 2,2',4,5,5'-penta-CB101, 2,3,3',4,4'-penta-CB105 and 2,3',4,4',5-penta-CB118), and PBDE (4,4'-di-BDE15, 2,4,4'-tri-BDE28, 2,2',4,4'-tetra-BDE47, 2,2',4,5'-tetra-BDE49, 2,2',4,4',5-penta-BDE99, 2,2',4,4',6-penta-BDE100, 2,2',4,4',5,5'-hexa-BDE153, 2,2',4,4',5,6'-hexa-BDE154 and 2,2',3,4,4',5',6-hepta-BDE183) congeners using hepatic microsomes of a beluga whale (Delphinapterus leucas) from the Arviat (western Hudson Bay) area of the Canadian Arctic. Ortho-meta bromine-unsubstituted BDE15, BDE28 and BDE47 were significantly metabolized (100%, 11% and 5% depleted, respectively) by beluga, whereas control rat microsomes (from pooled male Wistar Han rats) metabolized BDE28, BDE49, BDE99 and BDE154 (13%, 44%, 11% and 17% depleted, respectively). CB15 and CB77 (putative CYP1A substrates) were more rapidly metabolized (100% and 93% depleted, respectively) by male beluga than CB26 and CB31 (CYP1A/CYP2B-like) (25% and 29% depleted, respectively), which were more rapidly metabolized than CB52 (CYP2B-like) (13% depleted). Higher chlorinated CB101 and CB105 showed no depletion. Rat control microsomes metabolized CB15 to a lesser extent (32% depleted) than beluga, but much more rapidly transformed CB52 (51% depleted, respectively). Within the 90 min in vitro assay time frame, the preference was towards metabolism of ortho-meta unsubstituted congeners (for both PCBs and PBDEs) in beluga whale, whereas for rat controls, meta-para unsubstituted congeners also substantially metabolized. For both beluga whale and rat, metabolic rates were inversely associated with the degree of halogenation. For the rapidly biotransformed CB15 and BDE15, water-soluble OH-metabolites were detected after incubation. These results indicate that CYP-mediated oxidative hepatic biotransformation is a metabolic pathway in the toxicokinetics of both PCB and PBDE congeners in beluga whales and in the rat model. This may suggest that the formation of potentially toxic oxidative PCB and PBDE products (metabolites), in addition to the parent pollutants, may be contributing to contaminant-related stress effects on the health of beluga whale.