This book examines the way in which Robert Boyle seeks to accommodate his complex chemical philosophy within the framework of a mechanistic theory of matter. More specifically, the book proposes that Boyle regards chemical qualities as properties that emerge from the mechanistic structure of chymical atoms. Within Boyle’s chemical ontology, chymical atoms are structured concretions of particles that Boyle regards as chemically elementary entities, that is, as chemical wholes that resist experimental analysis. Although this interpretation of Boyle’s chemical philosophy has already been suggested by other Boyle scholars, the present book provides a sustained philosophical argument to demonstrate that, for Boyle, chemical properties are dispositional, relational, emergent, and supervenient properties. This argument is strengthened by a detailed mereological analysis of Boylean chymical atoms that establishes the kind of theory of wholes and parts that is most consistent with his emergentist conception of chemical properties. The emergentist position that is being attributed to Boyle supports his view that chemical reactions resist direct explanation in terms of the mechanistic properties of fundamental particles, as well as his position regarding the scientific autonomy of chemistry from mechanics and physics.