<jats:title>Abstract</jats:title><jats:p>A key goal of coral restoration is to re-establish self-sustaining coral populations and ensure resilience to future stressors, which requires that genetic diversity is maximised. However, coral genetic and genotypic (clonal) diversity is variable across reef sites via success of sexual recruitment, and cryptic species diversity can complicate breeding efforts. Assessing genotypic and genetic diversity of colonies to be used in restoration is therefore critical to avoid founder, inbreeding or outbreeding effects. Considering recent efforts to upscale coral propagation on the Great Barrier Reef (GBR), we examined species, population and clonal structure of a commonly out-planted tabular <jats:italic>Acropora</jats:italic> species—<jats:italic>Acropora hyacinthus</jats:italic> (Dana, 1864). A total of 189 colonies were sampled from six reef systems throughout the northern-central GBR and genotyped using an <jats:italic>Acropora-</jats:italic>specific Affymetrix microarray, which resulted in 1387 variant sites that passed quality control. Cryptic species were readily resolved and all sampled <jats:italic>A. hyacinthus</jats:italic> colonies represented unique genotypes within sites at three reefs. At reefs that contained multi-ramet genets (clonal genotypes), the mean and maximum between-ramet distances were 0.68 and 1.99 m, respectively. Therefore, sampling colonies &gt; 2 m apart increases the likelihood these colonies represent distinct genets. Such a sampling design therefore maximises genotypic diversity when sourcing colonies for propagation and out-planting. Based on these variant sites, we found no between-reef genetic divergence based on locality. Furthermore, through unintentional sampling of non-target tabular Acroporid species, we show how this genotyping method may be used for resolving taxonomic uncertainty as well as population dynamics.</jats:p>