How is it possible that in Three Essays on Religion Stuart Mill gives more credit to the design argument than to the Darwinian explanation of biological adaptations? Three main types of reasons are presented. The first derives from the theory of knowledge contained in A system of logic and Mill’s understanding of both Darwin and Design: making use of the method of agreement, the design argument is an instance of genuine inductive reasoning, which for Mill is basically sound, while Darwin follows the “hypothetical method” that Mill disvalues. Moreover, the whole Darwinian strategy, inherited from Whewell’s view of consilience, is foreign to Mill’s view of science. The second type of reasons derives from Mill’s metaphysics: within his phenomenalist framework, Mill is not committed to a naturalistic ontology, and he has no reason to favor the elimination of the supernatural. Finally, fruitfulness is not a key epistemic value for him, and Mill’s reservations on Darwin mirror the limitations of his own epistemic norms.