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Freshwater eels, genus Anguilla, have a distinctive catadromous life history, which could be associated with certain oceanic current systems and offshore spawning sites. Thus, migration and dispersion patterns are believed to be important factors influencing the population structure of each species. Temperate eel species are well studied, while little research has been conducted on the tropical counterparts that comprise two-thirds of all eel species. The population structure of three tropical species, A. marmorata, A. bicolor bicolor and A. bengalensis bengalensis, which are distributed widely in the Indo-Pacific region, were explored by means of DNA sequence analysis of mitochondrial cytochrome c oxidase subunit I (COI). This study suggests that A. bicolor bicolor might have two genetically distinct populations (fixation index, FST = 0.891; p < 0.001) that co-occur geographically in the Indo-Pacific region, while A. marmorata and A. bengalensis bengalensis might have a panmictic-population structure in this region. This study is the first to explore the population genetic structure of A. bengalensis bengalensis. The present results also suggest plausible dispersion and migration of these tropical species into their continental habitats.