Contamination status of brominated flame retardants (BFRs) and persistent organic pollutants (POPs) in blubber of finless porpoises (Neophocaena phocaenoides) stranded along the coasts of Seto Inland Sea and Omura Bay in Japan were investigated. Levels of PCBs, DDTs and CHLs were significantly higher than those of HCHs, HCB, PBDEs and HBCDs. Concentrations of PBDEs and HBCDs, as well as organochlorine compounds in males increased with body length (p < 0.05). Among 14 PBDE congeners analyzed, BDE-47 was the predominant, which is similar to those generally reported in biota. PBDEs, HBCDs and PCBs showed no obvious temporal trend in concentrations during the study period, suggesting continuous environmental release of these chemicals. On the other hand, levels of DDT, CHLs and HCHs have decreased. Concentrations of PCBs in liver trematode infected individuals were significantly higher than those in not infected individuals, implying there could be a relationship between contaminant levels and parasitic infection.