In this chapter, we will explain what a phylogenetic tree represents and introduce methods that can be used for constructing phylogenetic trees from genetic data from pathogens. Tree-like descriptions have been used extensively from the beginning of modern biology in the eighteenth century to describe the relatedness patterns between organisms, but their mathematical formalisation is only recent. We overview the main concepts and methods to reconstruct phylogenetic trees from genomic data. We outline important considerations when building phylogenetic trees, including the biology of the organism, the preparation of the input alignment, possible methods employed for tree-building and considerations for downstream inference and epidemiological insights. Important concepts described in this chapter will include terminology used when discussing phylogenetic trees, appropriate rooting of phylogenetic trees, assessing statistical confidence in reconstructed phylogenies and the requirements and approaches for building time-calibrated phylogenetic trees and transmission trees. Throughout, emphasis will be placed on the need for critical appraisal of the output from phylogenetic inference, including thorough evaluation of limitations to ensure the reliability of epidemiological findings. We provide an overview of applications of phylogenetic methods in infectious disease epidemiology to describe the dynamics of infectious disease outbreaks and epidemics, or to test specific hypotheses, such as the evolutionary origin of a zoonotic pathogen. The reader will become acquainted with key applications of phylogenetic inference in infectious disease epidemiology and be provided with a tutorial, walking stepwise through a typical phylogenetic analysis.