Mitochondrial DNA (mt‐DNA) of three eel species (the Atlantic eelsAnguilla anguillaandA. rostrata, and the African eelA. mossam‐bica), was sequenced and compared with mt‐DNA of other Indo‐Pacific eels(A. japonicaandA. marmorata, obtained from the EM‐BL data library), with the aim of analysing their phylogenetic relationships. Maximum parsimony analysis of 475 bp alignable sequences (partial Cyt‐b, tRNAThrand tRNAPro) showed a single most parsimonious tree, which was in agreement with the phylogeny ex pected on the basis of their breeding grounds distribution. UPGMA analysis resulted in a similar tree. Pairwise comparison of the se quences confirmed te genetic separation of the Atlantic species and showed a small evolutive distance between them. Nucleotide diver sities between Indo‐Pacific species equaled the diversities between these and the two grouped Atlantic species, suggesting that the three Indo‐Pacific species could have had an evolutive origin almost con temporary with a common ancestor of the Atlantic eels. A further 922 bp alignable mt‐DNA sequences (partial D‐Loop, tRNApheand 12srDNA)of A. rostrata, A. anguillaand Amossambicaconfirmed the phylogenetic relationships among the three species, but showed a slower mutation rate compared with the previous sequences, point ing to a non‐random distribution of variable sites along the mitochondrial genome. The possible geological events responsible for eel speciation are discussed.