This document summarizes a study on changes in benthic fauna in the inner part of Ariake Bay between 1989 and 2006. The mean number of species, abundances, and biomass of macrobenthos declined significantly over this period. Benthic communities shifted from large, long-lived species to smaller, short-lived species, indicating long-term organic pollution. Distribution of dominant bivalve species also changed. The deterioration of the benthic ecosystem is likely due to increased hypoxia, sediment changes, and pollution stressors in the bay. Continued monitoring is needed to inform management decisions for restoring marine ecosystems and benthic habitats in Ariake Bay.