<p><span style="font-size:14px"><span style="font-family:Arial,Helvetica,sans-serif">The establishment of a conservation strategy or restoration goal for river estuaries requires knowledge of potential biota or possible habitat characteristics. In this study, we investigated the relationship between estuarine fauna and macro scale physical indicators on Kyushu Island, Japan to provide basic information for estuarine conservation. As a result of the classification of shellfish fauna by similarity, the Kyushu region was divided into three groups, namely, 1) southern Kyushu with high wave exposure, long fetch, and low tidal variation; 2) the Ariake and Yatsushiro seas with low wave exposure, short fetch, and high tidal variation; and 3) northern Kyushu with an intermediate fetch and tidal variation. In addition, a number of sites, such as Nakatsu Port, Sone tideland, and the Honmyou River, were classified into geographically different groups. This is because the physical characteristics of these sites were similar to classified groups or shellfish fauna were significantly altered by artificial impacts. As a result of discriminant analysis, the discrimination hit rate of species inhabiting the inner bay or tidal flat was high, whereas that for species using a wide variety of bottom sediment environment was low. To improve the accuracy of the discriminant model, it is necessary to collect more detailed physical information, such as habitat type, salinity concentration, or grain diameter of bottom sediment. To establish a conservation or restoration strategy, there is a need for classifying taxonomic groups or physical characteristics.</span></span></p>