The pigmentation stages of Anguilla japonica were classified from the glass eel to yellow eel stage using 412 wild-caught eels from Hamana Lake and detailed developmental observations of 10 laboratory-reared eels. The sequential appearance of pigment was similar to that in A. anguilla, except for delayed pigment formation on the nerve cord of A. japonica. The general classification of pigmentation stages (VA–VIB) in A. anguilla was applicable to A. japonica, but the VB stage could be separated into two stages (VB1, VB2) in A. japonica. The completion of guanine deposition on the intra-abdominal membrane may be a trait to discriminate the yellow eel stage (VII) from the VIB stage. In natural conditions, wild-caught 0-age eels (n = 3,298) did not increase in size and retained a slender body form until VIA4, and then became thicker during VIB. The transition between body forms and growth may correspond to their ecological change from using passive transport in glass eels with tidal flow into rivers, to their settlement and further movements of elvers upstream. Considering this behavioral transition and pigmentation progression, it is proposed that the terms "glass eel" and "elver" could be defined as stages VA–VIA4 and VIB, respectively.