Newton famously rejected the use of hypotheses in natural philosophy, in stark contrast to many of his contemporaries, such as Descartes, Huygens, and Leibniz, who employed hypothetical methods. This disagreement is often framed as one concerning the Hypothetico-Deductive (HD) method, but I argue that this is mistaken. The relevant hypothesis-based methods at issue were what I call inference to the best hypothesis and its stronger version, inference to the only plausible hypothesis. These methods were far more nuanced and plausible than HD, and they enjoyed widespread popularity among early modern thinkers, even among prominent experimental philosophers. Newton rejected them nonetheless.