The COVID-19 crisis in France necessitated the rapid establishment of a genomic surveillance system at the national and regional levels to assess its impact on public health: the EMERGEN consortium (Consortium for Surveillance and Research on Infections Caused by EMERgent Pathogens via Microbial Genomics). Santé publique France’s activities related to this consortium were funded by various sources, including the SEQ4EPI project (Sequencing pathogens for epidemiology). Building on the experience with SARS-CoV-2, the EMERGEN consortium enabled the development of a robust sequencing infrastructure, incorporating a national genomic database (EMERGEN-DB), bioinformatics tools, and a network of sequencing laboratories. Initially focused on tracking SARS-CoV-2 variants, this model demonstrated in 2024 its ability to adapt to other pathogens, notably the monkeypox virus (Mpox) and zoonotic influenza. This document explores strategies for genomic surveillance of emerging pathogens, drawing on lessons learned during the COVID-19 pandemic. It proposes a methodological framework for extending these tools to other priority pathogens, incorporating a "One Health" approach to coordinate human, animal, and environmental health. This guide summarizes the critical challenges: developing decision-making tools for public health professionals, structuring interdisciplinary collaborations, and developing standardized approaches to respond rapidly to health emergencies. Based on real-world scenarios, it proposes a methodology adaptable to any outbreak. In conclusion, this document highlights the importance of close coordination among epidemiologists, microbiologists, and international stakeholders to anticipate global health threats. It offers a practical guide for integrating genomics into the surveillance of emerging pathogens, while ensuring a balance between operational efficiency and compliance with European data protection regulations.