The reef condition and resilience of the Great Barrier Reef is under threat due to climate change and other influences. Coral populations at Magnetic Island are further impacted by regional and local stressors, all of which contribute to a poor reef health condition. Recent demographic analysis revealed that Magnetic Island populations of the dominant reef-building species Acropora tenuis may have experienced bottleneck events in the past, which have resulted in small effective population size. Genetic connectivity analyses of corals across the GBR raise concern that Magnetic Island populations may be genetically isolated from adjacent fringing reefs, which poses additional threats to the survival of populations. However, studies involving A. tenuis at Magnetic Island have not provided tangible evidence that Magnetic Island populations are under increased threat due to a reduction in their genetic diversity or isolation. Therefore, a fine-scale analysis has been conducted assessing the population structure and genetic diversity of A. tenuis populations surrounding Magnetic Island, which assists in identifying their genetic connectivity to surrounding populations. This knowledge is crucial to underpin the management of local reefs to inform management strategies of how to best prevent further loss and promote resilience to environmental challenges.