Like many fishes on coral reefs, the false clown anemonefish, Amphiprion ocellaris, has a life history with two different phases: adults are strongly site attached, whereas larvae are planktonic. Therefore, the larvae have the potential to disperse, but the degree of dispersal potential depends primarily on the period of the larval stage, which is only 8–12 days in A. ocellaris. In this study, we investigated the genetic population structure and gene flow in A. ocellaris across the Indo-Malay Archipelago by analysing a fragment of the mitochondrial control region. Population genetic analysis, using amova, revealed a significant and high overall ΦST-value of 0.241 (P < 0.001), clearly showing limited gene flow. Haplotype network analysis detected eight distinct clades corresponding mainly to different geographical areas, which were most probably separated during sea level low stands in the Pleistocene. The distribution of the clades among the different populations indicated slow partial re-mixing mainly in the central region of the archipelago. Major surface currents seem to facilitate larval dispersal, indicated by higher connectivity along major surface currents in the region (e.g. Indonesian Throughflow). Four main groups were found by the hierarchical amova within the archipelago. These different genetic lineages should be managed and protected as separate ornamental fishery stocks and resource contributing to the genetic diversity of the area. Regarding the high diversity and the differentiation among areas within the Indo-Malay Archipelago of A. ocellaris populations, the centre-of-origin theory is supported to be the main mechanism by which the high biodiversity evolved in this area.