Major threats to marine species and ecosystems include overfishing, invasive species, pollution and climate change. The changing climate not only imposes direct threats through the impacts of severe marine heatwaves, cyclones and ocean acidification but also complicates fisheries and invasive species management by driving species range shifts. The dynamic nature of these threats means that the future of our oceans will depend on the ability of species to adapt. This has led to calls for genetic interventions focussed on enhancing species' adaptive capacity, including translocations, restocking and selective breeding. Assessing the benefits and risks of such approaches requires an improved understanding of the genetic architecture of adaptive variation, not only in relation to climate-resilient phenotypes but also locally adapted populations and the fitness of hybrids. Large structural genetic variants such as chromosomal inversions play an important role in local adaptation by linking multiple adaptive loci. Consequently, inversions are likely to be particularly important when managing for adaptive capacity. However, under some circumstances, they also accumulate deleterious mutations, potentially increasing the risk of inbreeding depression. Genetic management that takes account of these dual roles on fitness is likely to be more effective at ensuring population persistence. We summarise evolutionary factors influencing adaptive and deleterious variation of inversions, review inversions found in marine taxa, and provide a framework to predict the consequences of ignoring inversions in key management scenarios. We conclude by describing practical methods to bridge the gap between evolutionary theory and practical application of inversions in conservation.