<p>The respiratory microbiome plays a critical role in the health of organisms and studying it in natural populations can reveal interactions between hosts and their environment, as well as help predict responses to environmental stressors. We characterized the core respiratory bacteriome and functional profiles of Eastern North Pacific blue whales (<i>Balaenoptera musculus</i>) sampled in the Gulf of California using next-generation sequencing. Our compositional analysis identified 15 dominant bacterial phyla in the respiratory tract, with Proteobacteria (34.44%), Firmicutes (26.98%), Bacteroidota (20.26%), Fusobacteriota (7.61%), and Actinobacteria (5.55%) as the most abundant. Nineteen ASVs, representing 12 bacterial genera (primarily <i>Corynebacterium</i>,<i> Oceanivirga</i>,<i> Tenacibaculum</i>, and <i>Psychrobacter</i>), were shared by over 60% of whales, with a relative abundance greater than 0.02%. These bacteria, proposed to be the core respiratory bacteriome of blue whales, contributed to functional pathways associated with metabolism, environmental information processing, and cellular processes. Notably, two whales with high relative abundance of <i>Mycoplasma</i> spp. and of <i>Streptococcus</i> spp., exhibited overrepresented pathways related to nucleotide metabolism and translation, suggesting a suboptimal immune status or dysbiosis. To our knowledge, this is the first functional profiling of the bacteriome in any cetacean. Future studies are needed to explore how the blue whale respiratory bacteriome may vary over time, seasonally or across geographical locations. This study establishes a baseline for future research on the plasticity of the bacteriome, its associations with other microbiome components, the impact of environmental changes on its diversity, and its relevance for health. Our novel approach underscores the ecological and physiological importance of the bacteriome and its potential for long-term monitoring of a sentinel marine species in a rapidly changing ocean.</p>