In addition to unintentional formation of polychlorinated (PCDD/Fs), polybrominated (PBDD/Fs), and mixed halogenated (PXDD/Fs) dibenzo-p-dioxins/dibenzofurans during industrial activities, recent studies have shown that several PBDD and PXDD congeners can be produced by marine algal species from the coastal environment. However, multiple exposure status of anthropogenic and naturally derived dioxins in marine organisms remains unclear. The present study examined the occurrence, geographical distribution, and potential sources of PCDD/Fs, PBDD/Fs, and PXDD/Fs using mussels and brown algae collected in 2012 from Seto Inland Sea, Japan. The results showed the widespread occurrence of not only PCDD/Fs but also PBDDs and PXDDs in Seto Inland Sea. The geographical distribution pattern of PBDDs was similar to that of PXDDs, which were obviously different from that of PCDDs and PCDFs, and a significant positive correlation was observed between the levels of their predominant congeners, i.e., 1,3,7-/1,3,8-TrBDDs and DiBMoCDDs. Interestingly, potential precursors of 1,3,7-/1,3,8-TrBDDs and DiBMoCDDs, hydroxylated tetrabrominated diphenyl ethers (6-HO-BDE-47 and 2'-HO-BDE-68) and their mixed halogenated analogue (HO-TrBMoCDE), were also identified in the mussel and brown alga samples collected at the same site, by comprehensive two-dimensional gas chromatography with time-of-flight mass spectrometry (GC × GC-ToFMS) analyses. It is noteworthy that residue levels of 1,3,7-/1,3,8-TrBDDs and DiBMoCDDs in the mussel were 30 times higher than those in the brown alga, suggesting the bioaccumulation of these natural dioxins.