One of several important issues that inform contemporary philosophy of chemistry is the issue of structural explanation, precisely because modern chemistry is primarily concerned with microstructure. This paper argues that concern over microstructure, albeit understood differently than it is today, also informs the chemical philosophy of Robert Boyle. According to Boyle, the specific microstructure of ‘chymical atoms’, understood in geometric terms, accounts for the unique essential properties of different chemical substances. Because he considers the microstructure of ‘chymical atoms’ as semi-permanent, (...) Boyle considers these stable entities as operationally irreducible, even if they are not ontologically fundamental. While it is generally believed that our contemporary concern over structural explanation is a function of modern chemistry’s emphasis on microstructure, this discussion of structural explanation in Boyle will serve as a case study to illustrate the manner in which many of our contemporary concerns have deeply historical origins and the manner in which the history of chemistry can substantively inform issues in contemporary philosophy of chemistry. (shrink)