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The fungiid Heliofungia actiniformis is one of the most popular scleractinian coral species in the growing live aquarium trade, with the majority of specimens ori- ginating in Indonesia. Details on population connectivity may potentially provide important information with regards to harvest management efforts. Genetic structure was examined, using ribosomal ITS1, 5.8S and partial ITS2 sequences on a small scale among populations in the Spermonde Archipelago, South Sulawesi (up to 65 km distance, Ust = 0.09), and on a large scale throughout the Indo-Malay Archipelago (up to 2,900 km distance, Ust = 0.26). Significant genetic structuring was found at both scales. Within the Spermonde Archipelago isolation by distance as well as local oceanographic features shaped patterns of genetic connectivity. On the large scale, the data revealed genetically distinct populations in Tomini Bay, New Guinea and the Thousand Islands near Jakarta, and a lack of genetic differentiation among populations lying close to or directlyin the path of the Indonesian throughflow: from the central Visayas to the Flores Sea (Uct = 0.32). Whilst the influence of both historical and present day processes on genetic structuring of H. actini- formis populations was revealed, large scale results further emphasised the importance of oceanographic dynamics on larval dispersal patterns in this species. Potential for larval input from surrounding populations, and the increased vulnerability of upstream as well as isolated populations should be taken into consideration when setting future harvest quotas.