The historical movement of organisms, whether recent or in the distant past, forms a central aspect of evolutionary studies. Inferring patterns of migration can be difficult and requires reliance on a large suite of bioinformatic tools. As it is primarily the movement of groups of related individuals or populations that are of interest, population genetic and phylogeographic methods form the core of tools used to decipher migration patterns. Following a description of these tools, we discuss the most critical—and potentially most difficult—aspect of these studies: the inference process used. Designing a study, determining which data to collect, how to analyze the data, and how to coordinate these results into a coherent narrative are all a part of this inference process. Furthermore, using different types of data (e.g., genotypic and DNA sequence) from different types of sources (direct, or from the organisms of interest; and indirect, from symbiotic organisms) produces a powerful suite of techniques that are used to infer patterns of migration.