The Japanese mudskipper, Periophthalmus modestus, is classified as a semi-endangered species on the red list (2007) for estuarine and freshwater fishes published by the Ministry of the Environment. Information on the mudskipper in Hiroshima Prefecture is extremely scarce and it is not published in the red data book (2004) on Hiroshima Prefecture. To determine the current habitat of P. modestus, we surveyed 9 mudflat areas (including areas where the mudskipper had lived in the past) in Hiroshima Prefecture. Our surveys did not find even one fish in the western part of the survey area, while there were many fish found in the tidal flat of an eastern prefecture. In the central area, only young fish were recorded. This paper reports concretely that a critical situation exists for the mudskipper in their typical tidal flat habitat in Hiroshima Prefecture.