The population structure of the most widely distributed anguillid eel, Anguilla marmorata, was evaluated using a statistical analysis of total number of vertebrae. A total of 1166 specimens from 13 representative localities in the Indo-Pacific region from Réunion Island to Tahiti and from New Caledonia to Japan were examined in this analysis that also included previously published data. The specimens from Micronesia showed a remarkable difference from those collected at the 12 other localities, and those from Tahiti showed a significant difference from those collected at ten other localities, but not New Caledonia and Samoa. Furthermore, significant differences were found between the North Pacific Ocean region, except Ambon Island, and South Pacific Ocean regions and Réunion Island, while there were few differences between specimens from the Indian and South Pacific Ocean regions. It appears likely, based on this morphological analysis and the geographic range of this species, that there are at least four or more populations of A. marmorata as has been indicated previously by molecular genetic research.