An evaluation of ecological integrity is required for ecosystem conservation and restoration. The ecological region, or “ecoregion”, has been adopted as a unit of geological area to enable a comparison of the ecological integrity of different regions. The delineation of an ecological region is difficult in countries in East Asia, including Japan because of complex topographies (i.e., several peninsulas and islands) and fauna that are very finely delineated based on climate or geology. Therefore, it is important to appropriately determine the ecoregions when determining their biological integrity and comparing it among that of other ecoregions. I attempted to delineate an ecological region of the Japanese archipelago based on the similarities among fish fauna by integrating the information on fish fauna that was collected by the researchers and the national government and local governments. In addition, quantitative analyses to investigate the relationship between fish fauna classification and meteorological and geographical factors were conducted to discuss the factors that influence fish fauna classifications. The archipelago was classified into 15 fish fauna groups, and the results of these grouped classifications were closely related to the process by which the Japanese archipelago was formed, the ocean current in its coastal waters, and the connection of the water system to the glacial age. Our findings suggest that rivers within geographical areas that are different from those within the Japanese archipelago might have different fish fauna classifications based on our results and potential fish fauna depending on the characteristics of the watershed, such as the scale of the floodplain, river conflicts, or river formation process. By applying the results of our fish fauna classification, we are able to make a comparison of the biological integrity of fish fauna among different watersheds for managing the river environments or establishing conservation policies.
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