Climate change is altering species ranges, and abundances within ranges, as populations become differentially adapted and vulnerable to the climates they face. Hence, characterising current ranges, whether species harbour and exchange adaptive genetic variants, and how variants are distributed across landscapes undergoing rapid change, is crucial to predicting responses to future climates and informing conservation strategies. Such insights are nonetheless lacking for most species of conservation concern. We characterise genomic patterns of neutral variation, climate adaptation, and climate vulnerability (the amount of genomic change needed to track climate change by adaptation) in sister foundation species, the endemic marine tubeworms Galeolaria caespitosa and Galeolaria gemineoa, across a sentinel region for climate change impacts. First, species are shown to be partly sympatric despite previous support for non-overlapping ranges, and genetically isolated despite known capacity for hybrid crosses to yield viable early offspring. Second, species show signals of polygenic adaptation, but to differing components of temperature and involving mostly different loci. Last, species are predicted to be differentially vulnerable to climate change, with G. gemineoa — the less genetically diverse species — needing double the adaptation to track projected changes in temperature compared to its sister species. Together, our findings provide new insights into climate adaptation and its potential disruption by climate change for foundation species that enhance local biodiversity, with implications for evolutionarily-enlightened management of coastal ecosystems.