This chapter delves into phylogenetics, a crucial field in biological research that helps illuminate the evolutionary relationships among viruses. While the question of whether viruses should be classified as “living organisms” remains debated, evolution applies universally to all biological entities. Viruses, despite lacking certain characteristics of life, like a cellular structure, evolve through mechanisms of mutation and adaptation. Phylogenetics is key to understanding viral evolution by tracing evolutionary connections, investigating virus transmission patterns, and uncovering the molecular drivers of these changes. This chapter covers the essential steps in phylogenetic analysis, from dataset construction and tree reconstruction to statistical validation. It also examines various methods of phylogenetic tree construction, such as distance-based and character-based approaches, and explores DNA and protein evolution models. The chapter concludes with a case study on the evolutionary relationships among primate lentiviruses, demonstrating the value of phylogenetic analysis in understanding cross-species transmission and emerging infectious diseases. By analyzing these evolutionary links, scientists can gain insights into the origins and spread of new viral threats, underscoring the importance of phylogenetics in virology.