Botanical and zoological systematics in the early modern period – from Cesalpino in the sixteenth century to Linnaeus and Jussieu in the eighteenth century – was a two-faced and latently contradictory enterprise: It was, on the one hand, an empirical naturalistic science and, on the other hand, aligned with metaphysical principles concerning the order of natural things which form, according to these principles, a continuous chain of beings and a scala naturae, arranged according to degrees of their perfection. According to these principles, and especially according to that of continuity, no botanical or zoological classificatory system could establish anything but an artificial and unnatural order of plants and animals. The chapter illuminates these contradictions and tensions and traces the development of biological insights that eventually, at the turn of the eighteenth century, led systematists to renounce these metaphysical principles.