The Comparative Method in historical linguistics distinguishes resemblances among languages due to vertical transmission from those due to horizontal transmission, and from resemblances due to non-historical factors like chance. Alternative phylogenetic methods that seek long-range connections among languages have not been shown to consistently detect this distinction. Derived from the Comparative Method are the study of language contact and areal connections, lexicostatistical dating methods and linguistic-paleontological methods for reconstructing cultural knowledge. Methodological debates in historical linguistics, and application of these methods to cases in the linguistic history of the Southwest, are reviewed, suggesting that, in spite of the paucity of available data for many languages, historical linguistic methods have an important role to play in developing hypotheses about Southwestern prehistory.