Teleost gill is an important organ for osmoregulation. Different types of ionocytes are presented in the gill epithelium and they absorb ions in freshwater while excrete ions in seawater. The interchange between the ion-absorbing and ion-excreting ionocytes is crucial for the fish to survive salinity transfers. A transcriptomic approach was used to search for novel regulatory factors and transporters in the gill of euryhaline medaka and eel under a time-course seawater transfer.