Using the data recorded for 11 years from 1979 to 1989, characteristics of red tide occurrence were compared between Mikawa Bay and Shima-Watarai area in relation to the configuration of the bays and their physical and chemical environmental conditions. The average bloom citings per year (total number of days the red tide existed) in Atsumi Bay and Chita Bay, which are the branches of Mikawa Bay, were 183 days and 107 days, respectively. That in Shima-Watarai area was 126 days. The seasonal variation pattern of the red tide occurrence was similar in these areas, with the peaks in June and October. However, the composition of red tide forming taxa was different; flagellates were the major component in Shima-Watarai areas, while diatoms and flagellates occurred equally in Mikawa Bay. The configuration of the bay such as the mouth opening, depth and the volume which determine the residence time of water in the bay along with the amount of freshwater input is considered to be the important factor affecting the species composition. The residence time of water was significantly short in Ago Bay and Gokasho Bay, which are the inlets of Shima-Watarai area, compared to Atsumi Bay of eastern half of Mikawa Bay. The water quality of Mikawa Bay was also found to differ from that of Shima-Watarai area. Low temperature and low salinity in Mikawa Bay clearly reflects the influence of considerable amount of riverine inputs. On the other hand, influence of the Kuroshio water with high temperature and high salinity was obvious in Shima-Watarai area. The maximum nutrient concentration was higher in Shima-Watarai area than in Mikawa Bay, indicating the influence of the difference in the configuration of the bays. The effects of land use of the tributary area and the type of mariculture are also discussed.