The study of the evolutionary history of organisms by tracing them to common ancestors is known as phylogenetics. Over the last 20 years or so, the increasingly widespread availability of molecular data has seen the blossoming of methodologies for converting DNA information to evolutionary trees and networks. This article will attempt to give an overview of some of the methods that are available, covering data types, considerations for their use, and methods by which evolutionary ancestry can be reconstructed. Where relevant, the text will include examples of the use of these methodologies for the obligately biotrophic plasmodiophorids.