Emerging zoonotic diseases hold the potential to cause a major global public health threat; hence, there is an urgent need for their rapid and accurate detection, monitoring, and understanding of the pathogens at the molecular level. This chapter hence highlights the pivotal role of computational biology and bioinformatics resources in synergy with Next Generation Sequencing (NGS) technologies in combating such zoonotic diseases. This includes but is not limited to whole-genome sequencing, whole-exome sequencing, and metagenome sequencing; the technology provides deep insights into the ecology of pathogen evolution and transmission patterns as well as into genetic diversity. The technologies involved are indeed changing the complete scenario of disease surveillance, allowing, for instance, tracking in real-time pathogens and their markers of resistance to antibiotics. As part of the book, it will also go through some of the bioinformatics tools involved in the analysis of large-scale sequencing data understanding sequence alignment, variant calling, and functional annotation. For instance, NGS applications in zoonotic spill-over prediction, personalized therapeutic development, and response to public health measures will be enumerated. However, issues such as variability in data, high requirements for expertise in bioinformatics, and integration into public health systems continue. These can be mitigated by the standardization of data protocols, an increase in the bioinformatics training curriculum, and an improvement in interdisciplinary research collaboration. The global community will be best prepared to respond to emerging zoonotic disease threats by exploiting computational biology resources.