Understanding the evolutionary processes underlying population structuring of freshwater eels is an essential step toward comprehending their exceptional life cycle. However, in order to infer evolutionary scenarios that account for the genetic structure of current populations, it is necessary to unravel the history of gene flow from the onset of population divergence to the present. We used a combination of population-genetics methods and Bayesian coalescent analyses, to search specifically for the gene flow history that could explain contemporary genetic patterns of 2 Anguilla marmorata populations previously identified in the Indian Ocean. The population structure of A. marmorata was analyzed by genotyping 444 eels sampled from both sides of the Indian Ocean. Using 2 mitochondrial 16S rRNA single-nucleotide polymorphisms (SNPs) and 10 nuclear microsatellite loci, we first provided corroborative evidence of the existence of 2 genetic stocks: the Sumatran and the southwestern Indian Ocean (SWIO) populations (nuclear FST = 0.025 to 0.039). High frequencies of Sumatran haplotypes were found in SWIO localities (27 to 43%). Fitting the isolation-with-migration model to 16S rRNA sequence data led us to reject the hypotheses of inherited ancestral polymorphism and divergence with gene flow, but supported a recent secondary contact with unidirectional migration following a period of isolation. This scenario was confirmed by a cytonuclear disequilibrium found in SWIO, which also indicated that unidirectional migration was in progress. Finally, fitting simulated models of population composition to Bayesian assignments estimated from nuclear data suggested that Sumatran migrants are integrated in the SWIO breeding pool after their dispersal induced by the South Equatorial Current.