This chapter discusses Darwin’s lifelong interest in unconscious agency and instinct. Darwin typically treats instinct as a rational action that has become habitual and thus heritable; instinct embodies a cognitive process that does not know itself as such. His discussion of instinct is thus connected to other moments in his work where he uses the term ‘unconscious’; his treatment of previous taxonomists of species as unconsciously providing evidence for species transmutation, and his discussion of unconscious selection as an analogy for the effect of aesthetic preference in sexual selection. Darwin’s unconscious anticipates Freud’s as the embodiment of human agency in biological history.