FitzRoy's formal assignment was to chart coastal waters, but his hobby — passion really — was to seek out evidence for a literal, biblical interpretation of creation. That Darwin was trained for the ministry was central to FitzRoy's decision to have him aboard. That Darwin subsequently proved to be not only liberal of view but less than wholeheartedly devoted to Christian fundamentals became a source of lasting friction between them.

Darwin's time aboard HMS Beagle, from 1831 to 1836, was obviously the formative experience of his life, but also one of the most trying. He and his captain shared a small cabin, which can't have been easy as FitzRoy was subject to fits of fury followed by spells of simmering resentment. He and Darwin constantly engaged in quarrels, some "bordering on insanity," as Darwin later recalled. Ocean voyages tended to become melancholy undertakings at the best of times — the previous captain of the Beagle had put a bullet through his brain during a moment of lonely gloom — and FitzRoy came from a family well known for a depressive instinct. His uncle, Viscount Castlereagh, had slit his throat the previous decade while serving as Chancellor of the Exchequer. (FitzRoy would himself commit suicide by the same method in 1865.) Even in his calmer moods, FitzRoy proved strangely unknowable. Darwin was astounded to learn upon the conclusion of their voyage that almost at once FitzRoy married a young woman to whom he had long been betrothed. In five years in Darwin's company, he had not once hinted at an attachment or even mentioned her name.