Pathogen genetic data (PGD) serves as an invaluable source of epidemiological information. Genetic data enables the identification of etiological agents, determination of the spatial and temporal origins of outbreaks, investigations of transmission clusters, and estimation of epidemiological parameters, such as reproduction numbers and attack rates. With advancements in sequencing technologies and the potential of PGD to reveal essential epidemiological trends, genomics has become an essential tool for public health. Consequently, it has been deployed in response to multiple public health emergencies, including Ebola virus outbreaks in West Africa, Zika virus epidemics in the Americas, and most notably, the SARS-CoV-2 pandemic. In Brazil, genomic methods have been employed to characterize the epidemiological dynamics of both established and emerging viral threats, which have placed significant burdens on public health. This presentation will provide an overview of genomic epidemiology methods and tools, review their applications in Brazil, and advocate for potential approaches to address remaining knowledge gaps.