<p>Coastal coral reef ecosystems are experiencing increased environmental stress due to anthropogenic activity. Migration through larval dispersal is one of the mechanisms by which coral may be able to persist under such pressures. However, the genetic diversity and connectivity among coral populations from remote areas, such as Mozambique reefs, are not fully resolved. Patterns of water currents and eddies within the Mozambique channel potentially restrict larval dispersal between northern and southern coral populations. For these reasons, we hypothesized that (1) gene flow is restricted between southern and northern populations of <i>Acropora austera</i> in Mozambique; (2) genetic diversity is different between populations; (3) the extent of clonality influences the patterns of genetic diversity within and among populations. A total of 61 colonies of <i>A. austera</i> were sampled from six coral reefs and genotyped using restriction site-associated DNA sequencing (2b-RAD-Seq). The 2b-RAD-Seq libraries generated 10,371 SNP loci, from which population structure and genotypic and genetic diversity were estimated. Our results showed a clear genetic separation between southern and northern populations of <i>A. austera</i>. Populations from northern Mozambique, except for those from Vamizi and Memba, were more genetically diverse than population from the southern reef, Bazaruto. This restricted connectivity could be explained by the short pelagic larval duration of <i>A. austera</i> and/or by oceanographic factors, such as eddies in the Mozambique Channel. These data identified several potential vulnerable populations that should be considered in the implementation of adaptation strategies to preserve the coral reef ecosystems.</p>