The Coral Triangle region contains the world’s highest marine biodiversity, however, these reefs are also the most threatened by global and local threats. A main limitation that prevents the implementation of adequate conservation measures is that connectivity and genetic structure of populations is poorly known. The aim of this study was to investigate the genetic diversity, population structure and connectivity patterns of tropical corals in Indonesia on two different spatial scales, as well as by comparing two different reproduction strategies. Genotyping was based on microsatellite markers for 316 individual Seriatopora hystrix colonies and 142 Acropora millepora colonies sampled in Pulau Seribu and Spermonde Archipelago in 2012 and 2013. Differences in allelic diversity and a strong signature of divergence associated with historical land barriers at the Sunda Shelf were found for the brooding coral Seriatopora hystrix. However, differences in diversity and divergence were not pronounced in the broadcast spawning coral Acropora millepora. Within Spermonde Archipelago, two groups were identified: (1) sites of the sheltered inner-shelf and mid-shelf, which were found to be highly interconnected and (2) mid-shelf and outer-shelf sites characterised by higher differentiation. These patterns of contemporary dispersal barriers and genetic diversity can be explained by the differences in life history of the corals, as well as by oceanographic conditions facilitating larval dispersal. The contemporary dispersal barriers found within the Spermonde Archipelago emphasise the need for incorporating connectivity data in future conservation efforts.

珊瑚三角地区拥有世界上最高的海洋生物多样性，但是，这些珊瑚礁也是受到全球和当地威胁最大的威胁。阻止采取适当的保护措施的主要限制是，人们对种群的连通性和遗传结构知之甚少。这项研究的目的是在两个不同的空间尺度上研究印度尼西亚热带珊瑚的遗传多样性，种群结构和连通性模式，以及比较两种不同的繁殖策略。基因分型是基于微卫星标记的316个单个Seriatopora hystrix菌落和142个Acropora millepora在等位基因多样性，并与巽他陆架历史上的土地障碍相关的发散强烈签名2012年和2013年的差异岛Seribu和Spermonde群岛采样菌落发现育雏珊瑚Seriatopora锥。然而，在繁殖的产卵珊瑚Acropora millepora中，多样性和发散性的差异并不明显。。在Spermonde群岛内，确定了两个类别：（1）被遮蔽的内层货架和中层货架之间的位置相互关联，以及（2）以较高的分化度为特征的中层货架和外层货架。当代传播障碍和遗传多样性的这些模式可以通过珊瑚生活史的差异以及促进幼虫传播的海洋条件来解释。在Spermonde群岛内发现的当代传播障碍强调了在未来的保护工作中必须纳入连通性数据的必要性。