Edward Thorndike’s thesis can be considered the foundation document of modern comparative psychology. In it, Thorndike both rejected earlier anecdotal, anthropomorphic, and introspectionist approaches to the study of animal behavior and provided novel methods for studying comparative psychology that, 100 years later, are still the basis of the field. Thorndike also introduced ways of thinking about the relationship between evolutionary biology and comparative psychology that were to bedevil comparative psychologists for decades to come. Here the author discusses, from a contemporary perspective, both Thorndike’s lasting methodological and empirical contributions and his more problematic approach to the relationship between the study of phylogeny and comparative psychology.