Polychlorinated naphthalene (PCN) and polychlorinated biphenyl (PCB) congeners were measured in whole body and fillet of fish es collected from Michigan waters, including the Great Lakes, during 1996-1997. PCNs were found in all the fishes analyzed including those from Siskiwit Lake, a remote lake located near the southern shoreline of Isle Royale National Park in Lake Superior. Concentrations of total PCNs in fishes ranged from 19 to 31 400 pg/g, wet wt, and varied depending on sampling location and species. Fishes from the Detroit River contained the greatest concentrations of both PCNs and PCBs. Concentrations of total PCNs in fish es from Mi oh ig an waters we re significantly correlated with the concentrations of PCBs. As with total PCN concentrations, the profiles of PCN isomer/congener distribution in fishes varied among sampling locatio ns a nd species. Fishes from the Detroit River contained PCN profile similar to that of Halowax 1014, whereas those from Siskiwit Lake and Lake Superior contained greater proportions of congeners which have great bioaccumulative potential. Estimated concentrations of 2,3,7,8-tetrachlorodibenzo-p-dioxin equivalents (TEQs) of PCNs ranged from 0.007 to 11 pg/g, wet wt. PCN congeners 66/67 and 69 accounted for greater than 80% of the TEQs contributed by PCNs. TEQs contributed by PCBs, estimated based on H4IIE bioassay-derived TEFs, were in the range of 0.06-11 pg/g, wet wt, which were similar to those contributed by PCNs. When international TEFs (I-TEFs) for coplanar PCBs were applied, estimated PCB-TEQs ranged from 0.46 to 79 pg/g, wet wt, which were 5-10 times greater than those that were estimated from H4IIE TEFs. PCB congener 126 contributed greater than 50% of the TEQs contributed by PCBs in all the fishes. Overall, when similarly derived TEFs were used, PCNs contributed 2-57% of the sum of TEQs of PCNs and PCBs.