The merger of municipalities in the Heisei era, which was carried out nationwide beginning in FY 1999, combined 3,232 municipalities (at the end of FY 1998) into approximately 1,730 municipalities (at the end of FY 2009), before slowing down for a while. This study is designed to serve as the basis for closer research on the influence that the merger of municipalities in the Heisei era had on remote island municipalities. As such, it aimed to conduct an analysis of trends in the merger of remote island municipalities during the policy period. The remote island municipalities included in this study are 132 municipalities whose main land areas were located in islands that were not yet linked by bridge to the Japanese mainland as of the end of FY 1998. Also, the municipalities whose trends were studied were those for which the announcement of the merger of municipalities by the Minister for Internal Affairs and Communications was completed at the end of December 2009. The main results of the analysis are as follows. (1) There are 50 municipal entities that did not merge during the period of the merger of municipalities in the Heisei era. The number of remote island municipalities at the end of FY 2009 was roughly half of the number in existence at the end of FY 1998. (2) In terms of the rate of municipalities that merged, the trend for remote islands largely corresponds to the national trend. In other words, we can say that the merger of municipalities moved forward to a respectable degree in remote islands as well. (3) If we break down the merged remote island municipalities into patterns, we see that most are of the “one- island, one-municipality” or “belonging island” patterns. (4) Even among remote island municipalities that did not merge, 40% have established councils to conduct serious, detailed merger discussions. (5) Differences exist among prefectures in the progress of the mergers. Issues for future research include assessing the merger’s impact on the municipalities that merged, and an investigation into the ideal style of local government for the increasingly diverse remote island municipalities.