How Gregor Mendel (1822–1884) uncovered the rules of inheritance, which would later profoundly change biology, remains one of the greatest mysteries in the history of science. Because his work was rediscovered long after his death, few historical sources survive; by reinterpreting these and incorporating newly found materials, we argue that his discoveries likely arose from his plant-breeding programme. Stripping away later genetic concepts, we reexamine his experiments as he likely understood them, analysing his methods, data, reasoning and relationship to Charles Darwin and Carl Nägeli. We show that Mendel’s Pisum experiments remain highly relevant to today’s biology education.