Climate-driven changes in marine ecosystems are a pressing conservation concern impacting marine life, fisheries, and the communities that rely on them. This emphasizes the need to develop a deeper understanding of the risks to species and ecosystems in support of effective decision-making. For a large-bodied species of high commercial value such as Pacific bluefin tuna (Thunnus orientalis), intense fishing pressures compounded by the additive adverse effects of climate change pose a significant threat to the long-term sustainability of populations and fisheries they support. Here, we make use of a novel climate risk index for marine biodiversity that incorporates information on a species’ distribution, sensitivity to climate stressors, and adaptive capacity to environmental shifts to assess their vulnerability under contrasting emission scenarios (SSP5-8.5; high emissions and SSP1-2.6; high mitigation). Utilizing a generalized linear mixed model framework incorporating spatial random effects, we leveraged publicly available and validated occurrence records between the years 2000-2024 to model Pacific bluefin tuna habitat preferences across the Northwest Pacific Ocean. We utilized information on the species’ feeding ecology along with environmental predictors that accounted for the vertical dimension of the water column to predict suitable habitat for both surface waters (epipelagic layer; < 100 m) and at depth (mesopelagic layer; > 100 m). For each depth layer, we then used other open data sources to estimate climate vulnerability to the local persistence of Pacific bluefin tuna and the ecosystems they support throughout their geographic distribution. By mapping critical vulnerability areas for the species, we pinpoint locations likely to require additional intervention, such as the East China Sea and Northwest Pacific Basin. Our analysis contributes to the expanding body of research on the impacts of climate change on productivity and sustainability of key fisheries, emphasizing the need for adaptive management, conservation, and continuous monitoring to track shifts in climate vulnerability.