To understand the distribution, migratory behaviour and adaptation to salinity of Japanese eels Anguilla japocica in the coastal waters, five tagging methods were used, They were (1) liquid nitrogen marking on the fish body surface (2) fin clipped (3) oxytetracycline and alizarin complexone marking on otoliths (4) microchips and (5) coded wire tags. Totally, 4800 elvers and 2473 yellow eels were released into Da-pong Bay and Kao-ping River in 2002, 2003, 2005 and 2006. According to the recaptured data, the marked eels exhibited territory behaviours and most eels stayed within 1 km from the released sites. In addition, the Sr/Ca ratios also showed that most eels habituated in the estuarine areas.