1. For effective biodiversity conservation, verifying the correspondence of conservation sites among taxa and identifying the environmental characteristics of these sites are essential; however, only a few such studies have been performed in estuaries. The aim of the present study was to verify the surrogacy of estuarine gobies and crabs, to identify tidal rivers of high conservation priority, and to describe their environmental characteristics. 2. Distribution data for gobies and crabs were collected from 158 tidal rivers in the Kyushu region, Japan. Three conservation scenarios were analysed based on the distribution data of gobies alone, of crabs alone, and of both taxa, in order to assess the correspondence of the conservation candidates (i.e. tidal rivers) between taxa. 3. The degree of correspondence was poor for the candidates selected on the basis of the distribution data of gobies or crabs separately. More efficient candidates were selected based on the data for both taxa. The environmental characteristics of tidal rivers with high irreplaceability for conservation differed between the taxa. Tidal rivers forming and maintaining large tidal flats covered with fine sediment might have high irreplaceability for goby conservation, whereas rivers with saltmarshes connected to supratidal and intertidal zones might have high irreplaceability for crab conservation. 4. Tidal rivers with a high priority for conservation were identified by overlapping the candidates for three scenarios. These tidal rivers are not necessarily large, but have steep basins with river mouths that are less exposed to ocean waves. Moreover, the percentage of artificial areas in these rivers was low, suggesting that these rivers have not been exposed to excessive anthropogenic disturbance that leads to loss of estuarine habitat. 5. These results show that gobies and crabs are not surrogates for one another.