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Polymorphic microsatellite DNA parentage analysis was used to investigate the spatio-temporal variability of self-recruitment in populations of two anemonefishes: Amphiprion ocellaris and A. perideraion. Tissue samples of A. ocellaris (n = 364) and A. perideraion (n = 105) were collected from fringing reefs around two small islands (Barrang Lompo and Samalona) in Spermonde Archipelago, Indonesia. Specimens were genotyped based on seven microsatellite loci for A. ocellaris and five microsatellite loci for A. perideraion, and parentage assignment as well as site fidelity were calculated. Both species showed high levels of self-recruitment: 65.2% of juvenile A. ocellaris in Samalona were the progeny of parents from the same island, while on Barrang Lompo 47.4% of A. ocellaris and 46.9% of A. perideraion juveniles had parents from that island. Self-recruitment of A. ocellaris in Barrang Lompo varied from 44% to 52% between the two sampling periods. The site fidelity of A. ocellaris juveniles that returned to their reef site in Barang Lompo was up to 44%, while for A. perideraion up to 19%. In Samalona, the percentage of juveniles that returned to their natal reef site ranged from 8% to 11%. Exchange of progeny between the two study islands, located 7.5 km apart, was also detected via parentage assignments. The larger Samalona adult population of A. ocellaris was identified as the parents of 21% of Barrang Lompo juveniles, while the smaller adult population on Barrang Lompo were the parents of only 4% of Samalona juveniles. High self-recruitment and recruitment to nearby island reefs have important implications for management and conservation of anemonefishes. Small MPAs, preferably on every island/reef, should ensure that a part of the population is protected to enable replenishment by the highly localised recruitment behaviour observed in these species.

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 phi(ST)-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.