Scientific disagreements due to empirical problems—not enough data, not enough of the critical type of data, problems in analyzing the data—are generally short-lived and resolved in the next cycle of data production. Such disagreements are thus transitory in nature. Persistent scientific conflicts, on the other hand, do not necessarily mean some facts are correct and some are wrong, nor do they mean that we do not have enough information. More often, such persistent conflicts mean that the conceptual frameworks used by different groups of researchers are insufficient to resolve apparent conflicts in the data. The latter seems to be the case with persistent disagreements about the phenomenon of cospeciation, wherein there has historically been no framework that allows us to understand speciation by host switching when the host and parasite lineages involved are of equal ages. This situation can now be resolved with the emergence of what has become known as the “Stockholm Paradigm.” In short, re-examination of what has been dubbed the “classic case of cospeciation” shows that divergent views of cospeciation are subsumed and reconciled within the larger explanatory framework of the Stockholm Paradigm. The implications are considerable, given the need to have a fundamental understanding of faunal structure, assembly, and distribution in addition to an understanding of the historical and evolutionary drivers of diversity within the current arena of accelerating environmental change, ecological perturbation, and emerging infectious diseases.