Phylogenetics is the study and reconstruction of evolutionary history and is filled with numerous foundational issues of interest to philosophers. This paper briefly introduces some central concepts in the field, describes some of the main methods for inferring phylogenies, and provides some arguments for the superiority of model-based methods such as Likelihood and Bayesian methods over nonparametric methods such as parsimony. It also raises some underdeveloped issues in the field of interest to philosophers.