We investigated the occurrences of Noctiluca scintillans in the coastal waters of Harima-Nada, the Seto Inland Sea, using the red tide data set. These data concerned red tide occurrences that were reported in an annual report entitled “Red tides in the Seto Inland Sea” which was published by the Seto Inland Sea Fisheries Coordination Office of the Fisheries Agency, Ministry of Agriculture, Forestry and Fisheries of Japan. These data were imported into a geographic information system, and red tide areas were calculated. During the 26 years from 1979 to 2004, in the Seto Inland Sea, eutrophication improved, nutrient concentrations in seawater decreased dramatically, and the number of red tide occurrences excluding those concerning Noctiluca scintillans, decreased. However, the number of occurrences, area, and durations of Noctiluca scintillans red tides did not decrease. The ratio of Noctiluca scintillans red tides to total red tides for an average red tide index, which permits the assessment of spatial and temporal scales, was 54%. This was higher than that of the number of occurrences (36%). This indicates the importance of N. scintillans as a red tide organism.