The concentrations of polychlorinated dibenzo-p-dioxins (PCDDs), polychlorinated dibenzofurans (PCDFs), non-ortho polychlorinated biphenyls (non-ortho PCBs), and mono-ortho polychlorinated biphenyls (mono-ortho PCBs) in Japanese flounder (Paralichthys olivaceus, body length 10.4–36.6 cm) collected from Sendai Bay, Japan, were determined using high-resolution gas chromatography-mass spectrometry. The relationship between the concentrations of these compounds (dioxins) and the body length of the Japanese flounder was examined. The total PCDD and total PCDF concentrations did not correlate with body length (both r2 < 0.1, both p > 0.05), whereas the total non-ortho PCB and total mono-ortho PCB (coplanar polychlorinated biphenyls, Co-PCBs) concentrations were significantly correlated (r2
= 0.8, p < 0.05 and r2
= 0.63, p < 0.05, respectively). The bioaccumulation properties of PCDD/Fs in Japanese flounder differed from those of Co-PCBs. Toxicity equivalency quotient (TEQ) values derived from the Co-PCBs made up 46.3%–63.7% of the total TEQ value for all the dioxins. Although the concentrations of non-ortho PCBs were lower than those of mono-ortho PCBs, the TEQ value for non-ortho PCBs was higher than that for mono-ortho PCBs. The TEQ value for non-ortho PCBs increased more with increasing body length than did the values for PCDDs, PCDFs, and mono-ortho PCBs. These results show that from the standpoint of risk management, non-ortho Co-PCBs are the most important of the dioxins in Japanese flounder.