Coral reefs are threatened by climate change pressures, calling for urgent actions in carbon-emission reduction, ecosystem protection and restoration. Reef conservation must support the resilience of corals, influenced by their 1) genetic diversity and 2) tolerance to environmental changes that it encodes. The Reef Restoration and Adaption Program (RRAP) aims to maximise the resilience of multiple key coral species by considering their genetic make-up in 1) scalable conservation aquaculture, 2) targeted interventions such as assisted evolution, and 3) deployment of corals to suitable reef communities. To this end, quality assurance and quality control (QA/QC) on the genetic make-up of produced coral is critical to ensure that reef restoration efforts result favourably. For example, sequencing data revealed that even sexually-propagated corals can be genetically depauperate, which could be alleviated by selecting and breeding genotyped broodstock. QA/QC tools must be time-efficient to be useful in coral aquaculture practices, by employing rapid and scalable genetic sequencing techniques. Digital PCR-based eDNA assays on bacteria and eukaryotic pests are also established for corals cultured in high densities, to minimise the risk of infestation and transmission of problematic microorganisms into wild environments. These interventions and tools will help maximise eco-evolutionary impacts in our reef conservation efforts.