Shrimp are popular as food in Japan, but their contamination status is not well understood. In this study, 45 shrimp products (seven species) collected from eight locations in Japanese coastal waters and the South China Sea were analyzed for persistent organic pollutants (POPs) and naturally occurring halogenated contaminants (NHCs). The compounds with the highest mean concentration among shrimp species were endosulfans (4.0 ng g-1 dry weight, 41% of the total concentration), followed by polychlorinated biphenyls (PCBs, 26%), chlordanes (CHLs, 11%), methoxy-polybrominated diphenyl ethers (MeO-BDEs, 10%) and heptachlorinated methylbipyrrole (Cl7-MBP, 4%). Endosulfan concentrations were not correlated with the PCB and CHL concentrations, which suggested that these compounds had different sources and kinetics. Regional differences were observed in Sakura shrimp (Lucensosergia lucens), with higher concentrations of CHLs and Cl7-MBP from Suruga Bay in Japan, whereas MeO-BDEs were dominant in the south coast of Taiwan. The median estimated daily intake (EDI) of endosulfans through shrimp consumption was 60 pg kg-1 bw day-1. The EDIs of all analytes were well below reference doses set by the United States Environmental Protection Agency, indicating that health risks were unlikely, even in 95th percentile scenarios. The profiles and concentrations of these contaminants in shrimp in Japan suggest that shrimp is a potential dietary source of POPs (e.g., α-endosulfan) and NHCs (e.g., 2'- MeO-BDE68), and can serve as bioindicators of contamination status for dietary intake in Japan.