Identifying relevant knowledge to be used in conversational systems that are grounded in long documents is critical to effective response generation. We introduce a knowledge identification model that leverages the document structure to provide dialogue-contextualized passage encodings and better locate knowledge relevant to the conversation. An auxiliary loss captures the history of dialogue-document connections. We demonstrate the effectiveness of our model on two document-grounded conversational datasets and provide analyses showing generalization to unseen documents and long dialogue contexts.