Persistent organic pollutants, particularly polychlorinated dibenzo-p-dioxins (PCDDs), polychlorinated dibenzofurans (PCDFs), coplanar polychlorinated biphenyls (co-PCBs) and toxic equivalent quantity (pg TEQ g(-1)) were determined in sediment samples collected from Ariake Bay, Japan. The total concentration of PCDDs/DFs in surface sediment of the Yabe River (17,000 pg g(-1) dry wt) was approximately 2.5-fold higher than that of the Chikugo River (7,000 pg g(-1) dry wt) which has the highest flow amount of about 40% inputting to the northern Bay. The congener profile suggested that dioxin sources could be close to the study area. The PCDDs concentration (12,000 pg g(-1) dry wt) in the sediment layer, which was corresponding to the 1960s, was reflected on the pentachlorophenol (PCP) contamination occurring at that time in Ariake Bay. The reflecting of PCP in the sediment core was significantly considered by hierarchical cluster analysis. Based on isomer-specific analysis, the tetrachlorodibenzo-p-dioxin composition showed a gradual increase from 1978-1982 toward the surface, indicating that the pollution source at that period might be more influenced by chloronitrofen than PCP. This fact was supported, based on the ratio of Sigma PCDD to Sigma PCDF concentration. The PCDDs/DFs-derived TEQ contributed more than 90% of the SigmaTEQ (PCDDs/DFs and co-PCBs) in all the detected sediment layers. The contribution of PCBs to the total TEQ was low; however, an increasing historical trend of concentration was clearly observed.