Mitochondrial control region (mtDNA CR) diversity within and among 6 seahorse populations associated with the Indo-Pacific Hippocampus kuda complex (H. kuda from India, Malaysia, Indonesia and the Philippines, H. fuscus from the Red Sea and H. capensis from South Africa) was compared to determine whether there was support for the hypothesis that seahorses are able to colonize remote areas by means of rafting. Analyses performed on the data-set included phylogenetic reconstructions, estimation of relative population ages, tests for evidence of population expansion, pair-wise migration rates and divergence times, as well as relationships between genetic and geographic distances. The mtDNA data indicate that all populations have undergone recent expansions, but that the timing of these events differed. The H. kuda population from India was found to be the oldest, whereas the expansion of the H. fuscus population from the Red Sea took place most recently. The fact that all seahorse populations studied are characterized by a single ancestral mtDNA haplotype and migration rates are low in most cases, as well as the fact that no significant relationship between genetic and geographic distances was found, indicates that colonization of distant habitats by a small number of founding individuals may be common in seahorses associated with the H. kuda complex. As the level of subsequent gene flow among populations is low, this may result in rapid speciation.