 In this entry, we examine what phylogenetic inference is and how it works. In the first section, we briefly introduce the field of phylogenetics and its history. In section 2, we explore how phylogenetic inference provides useful problems for philosophers to examine, and where philosophical approaches have contributed to the scientific examination of phylogenetics. This will help display why phylogenetic inference is not merely a biological research problem, but a philosophical one as well. Finally in section 3, we will move to a discussion of some of the contemporary debates about foundational issues in phylogenetics, and what the future of phylogenetic inference looks like.