A standard line in the contemporary philosophical literature has it that physical theories are equivalent only when they agree on their empirical content, where this empirical content is often understood as being encoded in the equations of motion of those theories. In this article, we question whether it is indeed the case that the empirical content of a theory is exhausted by its equations of motion, showing that (for example) considerations of boundary conditions play a key role in the empirical (...) equivalence (or otherwise) of theories. Having argued for this, we show that philosophical claims made by Weatherall (2016) that electromagnetism in the Faraday tensor formalism is equivalent to electromagnetism in the vector potential formalism, and by Knox (2011) that general relativity is equivalent to teleparallel gravity, can both be called into question. We then show that properly considering the role of boundary conditions in theory structure can potentially restore these claims of equivalence and close with some remarks on the pragmatics of adjudications on theory identity. (shrink)