Concentrations, profiles and muscle-liver distribution of halogenated natural products (HNPs) and anthropogenic persistent organic pollutants (POPs) were investigated in five large pelagic fish species and one smaller planktivore fish species from the Western Indian Ocean. Analysis of swordfish muscle from the Seychelles revealed the predominance of HNPs, with the highest concentrations found for 2′-methoxy-2,3′,4,5′- tetraBDE (2′-MeO-BDE 68 or BC-2), 6-methoxy-2,2′,4,4′- tetraBDE (6-MeO-BDE 47 or BC-3) and 2,3,3′,4,4′,5,5′-heptachloro-1′-methyl-1,2′-bipyrrole (Q1), along with varied contributions of further HNPs. The mean concentration of ∑HNPs (330 ng/g lw) was one or two orders of magnitude higher than ∑DDTs (60 ng/g lw) and ∑PCBs (6.8 ng/g lw). HNPs (BC-2, BC-3 and Q1) were also predominant in individual samples of three tropical tuna species from the Seychelles and from other regions of the Western Indian Ocean (Mozambique Channel, off Somalia and Chagos Archipelago). Non-targeted gas chromatography coupled with electron capture negative ion mass spectrometry operated in the selected ion monitoring mode (GC/ECNI-MS-SIM) analysis of one swordfish sample indicated low abundance of rarely reported HNPs (three hexachloro-1′-methyl-1,2′-bipyrrole (Cl6-MBP) isomers and pentabromo-1,1′-dimethyl-2,2′-bipyrroles (Br5-DBP)) but no further abundant unscreened polyhalogenated compounds.