The population structures of two tropical species, Anguilla bicolor and Anguilla bengalensis, collected from several localities of each species range were evaluated using statistical analyses of total number of vertebrae (TV) data, which also included previously published data. There were significant differences in TV values between A. bicolor specimens from the Indian and Pacific oceans and between A. bengalensis specimens from the eastern and western Indian Ocean. These results suggest that A. bicolor is separated clearly into Indian Ocean and Pacific/Indonesian Seas populations and A. bengalensis has eastern and western populations in the Indian Ocean, which both correspond to the historical subspecies designations of these eels. The existence of different spawning populations of other species such as the widely distributed tropical eel A. marmorata raises the question about how to categorise these subspecies or populations. Regardless of the taxonomic category used, each of these spawning populations should be considered to be a distinct ecological unit for conservation and sustainable management purposes.