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Simple Summary: To understand the impact of climate change on marine mammals, we focused on the spotted seal population in the North Pacific. This ice-breeding species exhibits distinct variations across different regions. Our study aimed to quantify their ecological niches and conduct a conservation gap analysis. We found clear niche divergence among three populations and observed habitat contraction driven by climate change, potentially leading to breeding habitat loss in certain areas. Unfortunately, existing marine protected areas do not adequately cover most spotted seal habitats. By incorporating local adaptation into species distribution modeling, our research provides valuable insights for designing effective conservation policies to protect the different geographical populations of spotted seals in the face of climate change. This study highlights the importance of considering local adaptation in conservation and management strategies for marine mammal species. Local adaptation has been increasingly involved in the designation of species conservation strategies to response to climate change. Marine mammals, as apex predators, are climatechange sensitive, and their spatial distribution and conservation requirements are critically significant for designing protection strategies. In this study, we focused on an ice-breeding marine mammal, the spotted seal (Phoca largha), which exhibits distinct morphological and genetic variations across its range. Our objectives were to quantify the ecological niches of three spotted seal populations, construct the species-level model and population-level models that represent different regions in the Bering population (BDPS), Okhotsk population (ODPS) and southern population (SDPS), and conduct a conservation gap analysis. Our findings unequivocally demonstrated a clear niche divergence among the three populations. We predicted habitat contraction for the BDPS and ODPS driven by climate change; in particular, the spotted seals inhabiting Liaodong Bay may face breeding habitat loss. However, most spotted seal habitats are not represented in existing marine protected areas. Drawing upon these outcomes, we propose appropriate conservation policies to effectively protect the habitat of the different geographical populations of spotted seals. Our research addresses the importance of incorporating local adaptation into species distribution modeling to inform conservation and management strategies. [ABSTRACT FROM AUTHOR]