Mudflats are formed in the upper littoral zones in estuaries, especially in the innermost part of macro-tidal embayments (upper reaches of estuaries), providing a habitat for peculiar fauna and flora. The peculiar fauna and flora of estuarine mudflats appear to have been extirpated in many estuaries in Japan, along with the mudflats that have been damaged or destroyed by thoughtless and drastic coastal reclamation. At present, Ariake Bay, which constitutes the largest area of mudflats remaining in Japan, also has the greatest variety of species. The mudflat-specific species are almost or completely restricted to Ariake Bay, while populations of the same (or closely related) species are distributed along Asian continental coasts, which suggests they are continental relicts. Some of the mudflat-specific species now restricted to Ariake Bay (e.g.,the bivalve, Tegillarca granosa, the polychaete, Hediste japonica, the salt marsh plant, Suaeda japonica) previously enjoyed a wide distribution in Japan. Even within Ariake Bay, huge mudflats in Isahaya Bay were recently lost to a reclamation project there. The high productivity of benthic organisms in mudflats seems to benefit carnivores such as birds and fishes (e.g., Japanese eel). Conservation and restoration of mudflats are needed to conserve endangered species and to maintain traditional human fisheries and culture. From this aspect, restoration of the largest mudflats in Isahaya Bay in Ariake Bay is highly desirable.