This dataset comprises metagenomic data obtained from blood cell pellets of subantarctic marine birds inhabiting the Kerguelen Islands. Samples were collected between 2021 and 2023 as part of a non-invasive liquid biopsy approach to monitor avian health and microbiome composition. The study aims to explore the microbial diversity associated with these birds and assess potential biomarkers of health and environmental adaptation in subantarctic ecosystems.