Selecting candidate areas to protect the habitats of threatened freshwater fish species is a major challenge in urban areas. Therefore, we conducted a case study using a Marxan analysis based on fish fauna and land use data of five rivers flowing in the Fukuoka Plain, northern Kyushu Island, Japan, to construct priority maps to protect threatened freshwater fishes in the urbanized plain. We organized threatened fish fauna and land use data in the fourth-mesh scale, drawn as a 500-m square, resulting in 147 meshes with fauna and land use data. We assessed two cases—meshes were either analyzed as having the same cost (case 1) or having cost sizes classified into four classes based on cluster analysis of land use data (case 2). We divided the threatened species into those from either stream fish or floodplain fish and analyzed them separately. When meshes with high priority in both case 1 and case 2 were defined as primacy meshes for habitat protection, 10 and 28 meshes were identified in the stream and floodplain fish, respectively. Of the primacy meshes, 40 % for the stream fish and 54 % for the floodplain fish were distributed in urbanized areas, indicating that habitat protection was necessary in several urbanized areas on the plain. Meshes with low priority in case 1 and with high priority in case 2 were defined as the second most important meshes for habitat protection. The number of second most important meshes for the floodplain fish was smaller than that for the stream fish; therefore, the floodplain fish required habitat protection in urbanized areas to a greater extent than the stream fish.
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