Persistent organic pollutants (POPs) such as polychlorinated biphenyls (PCBs), dichlorodiphenyltrichloroethane and its metabolites (DDTs), polybrominated diphenyl ethers (PBDEs) and hexabromocyclododecanes (HBCDs) are known to be highly accumulated in cetaceans which are at the top of marine food webs. This study aimed to elucidate the interspecies difference and temporal trends of POPs levels in two offshore whale species inhabiting cold vs subtropical waters. Blubber samples of adult male Dall’s porpoises (Phocoenoides dalli) (n = 27) and melon-headed whales (Peponocephala electra) (n = 38) stranded from 1980 to 2019 were analyzed. Multiple linear regression models were used to analyze the temporal trends in POPs in the blubber. PCBs and DDTs followed significant decreasing trends since 1980s, but species differences in the trends of chlordanes (CHLs) and hexachlorocyclohexane isomers (HCHs) were observed. These results reflect the differences in the actual conditions of production and use of OCPs and the timing of their regulation in Japan and neighboring countries. In particular, concentrations of HCHs in Dall’s porpoises inhabiting cold waters have been unchanged since the 1980s and were an order of magnitude higher than those of melon-headed whales, indicating continued atmospheric transport and deposition to the cold open ocean. Interestingly, the concentrations of brominated flame retardants (BFRs), PBDEs and HBCDs, have significantly increased since the 1980s in both whale species, and the increasing trend continued after 2000 for HBCDs. These results imply that the migration of HBCDs into the open ocean is still ongoing.