Structures of polybrominated hexahydroxanthene derivatives (PBHDs) previously detected in commercial fish from the Mediterranean Sea and mussels from New Zealand were assigned to 2,7-dibromo-4a-bromomethyl-1,1-dimethyl-2,3,4,4a,9,9a-hexahydro-1H-xanthene (TriBHD) and 2,5,7-tribromo-4a-bromomethyl-1,1-dimethyl-2,3,4,4a,9,9a-hexahydro-1H-xanthene (TetraBHD) by comparing their gas chromatography/mass spectrometry (GC/MS) features with isolates from an Australian sponge of the Cacospongia genus. Because of the geographic distance between the Mediterranean Sea in Europe (origin of the fish) and Australia (origin of the sponge), a closely related sponge, Scalarispongia scalaris, was collected in the Mediterranean Sea and analyzed for PBHDs and other halogenated compounds. The Mediterranean sponge contained the PBHDs at 37 mg/kg dry weight. Using quantitative standards for the first time, the PBHD concentrations in fish and mussel samples published earlier were re-examined. Concentrations of up to 1 mg/kg TriBHD and 0.5 mg/kg TetraBHD were determined in the lipids. No correlation with 2,2′, 4,4′, 5,5′-hexachlorobiphenyl (PCB 153) or p,p’-DDE was found, which is in agreement with other marine halogenated natural products detected in the fish samples. Besides the PBHDs, further unknown halogenated compounds were detected in the Mediterranean sponge, some of which were also detected in commercial fish. GC/electron ionization-MS analysis showed that a major mixed-halogenated compound in the sponge had a molecular ion at m/z 480 and contained three bromines, three chlorines, and 9–10 carbons. No corresponding structure has been described for this feature in the scientific literature. This sponge secondary metabolite and potential novel halogenated natural product was also detected in commercial fish. Another prominent mixed halogenated compound detected both in sponge and fish was the dibromotrichloro monoterpene MHC-1 (C10H13Br2Cl3).