Climate change is causing unprecedented alterations to marine ecosystems through rising temperatures, ocean acidification, and deoxygenation, threatening global marine biodiversity. Recent advances in genomic technologies have revolutionized our understanding of how marine species respond to these environmental stressors at the molecular level. This comprehensive review synthesizes current knowledge on genomic, transcriptomic, and epigenomic responses of marine organisms to climate change, with particular emphasis on adaptive evolution, phenotypic plasticity, and evolutionary rescue. We examine case studies across taxa including corals, fish, mollusks, and phytoplankton, highlighting conserved and taxon-specific stress response mechanisms. Furthermore, we discuss emerging conservation strategies informed by genomic data, such as assisted gene flow and genomic selection, and propose a framework for integrating multi-omics approaches with ecological modeling to predict and mitigate biodiversity loss in changing oceans.