Euryhaline teleosts exhibit varying acclimability to survive in environments that alternate between being hypotonic and hypertonic. Such ability is conferred by ion channels expressed by ionocytes, the ion-regulating cells in the gills or skin. However, switching between environments is physiologically challenging, because most channels can only perform unidirectional ion transportation. Coordination between acute responses, such as gene expression, and long-term responses, such as cell differentiation, is believed to strongly facilitate adaptability. Moreover, the pre-acclimation to half seawater salinity can improve the survivability of Japanese medaka (Oryzias latipes) during direct transfer to seawater; here, the ionocytes preserve hypertonic acclimability while performing hypotonic functions. Whether acclimability can be similarly induced in a closed species and their corresponding responses in terms of ion channel expression remain unclear. In the present study, Japanese medaka pre-acclimated in brackish water were noted to have higher survival rates while retaining higher expression of the three ion channel genes ATP1a1a.1, ATP1b1b, and SLC12a2a. This retention was maintained up to 2weeks after the fish were transferred back into freshwater. Notably, this induced acclimability was not found in its close kin, Indian medaka (Oryzias dancena), the natural habitat of which is brackish water. In conclusion, Japanese medaka surpassed Indian medaka in seawater acclimability after experiencing exposure to brackish water, and this ability coincided with seawater-retention gene expression.