The genus Anguilla Shaw of Family Anguillidae consists entirely of freshwater eels, including 15 species and 2 subspecies. Conventionally, variegated markings and the length of the dorsal fin are the major morphological features used for reconstruction of phylogenetic relationships. The evolutionary history of these species remains unclear, especially for the Atlantic eels, whose habitats are far from the Metropolis in the Indo-Pacific region. This study reexamined the phylogenetic relationships of 12 Anguilla species by sequencing of the cytochrome b and 12S rRNA genes. In our analysis, species bearing similar coloration patterns or dorsal fin morphology are not necessarily clustered in the same clade, indicating that these morphological features might be unstable or might have occurred independently in different lineages during evolution. Combining our molecular data and geographical evidence, we speculate that (1) Anguilla first radiated about 20 million years ago, (2) the ancestors of Atlantic eels did not migrate by drifting through the Tethys Seaway at the leptocephali stage but instead trekked across the Central American Isthmus to the Sargasso Sea for spawning at the adult stage, and (3) multiple radiation events had occurred at the Metropolis during Anguilla evolution.