Philosophical treatments of scientific controversies usually focus on theory, excluding important practice related aspects. However, scientists in conflict often appeal to extra-theoretical and extra-empirical elements. To understand better the role that non-empirical elements play in scientific controversies, we introduce the notion of borrowed epistemic credibility , illustrating our proposal with a recent controversy in a field of evolutionary biology known as phylogeography. Our analysis shows how scientific controversies that spring from disagreements about methodological issues potentially involve deeper debates regarding what constitutes good science, prompting the re-examination of more general issues, such as the nature of inference, rationality, and objectivity.