Undergraduate theses and other capstone research projects are standard features of many science curricula, but participation has typically been limited to only the most advanced and highly motivated students. With the recent push to engage more undergraduates in research, some faculty are finding that their typical approach to working with thesis writers is less effective, given the wider diversity of students, or is inefficient, given the higher participation rates. In these situations, a more formal process may be needed to ensure that all students are adequately supported and to establish consistency in how student writers are mentored and assessed. To address this need, we created BioTAP, the Biology Thesis Assessment Protocol, a teaching and assessment tool. BioTAP includes a rubric that articulates departmental expectations for the thesis and a guide to the drafting-feedback-revision process that is modeled after the structure of professional scientific peer review. In this article we (a) describe BioTAP's parts and the rationale behind them, (b) present the results of a study of the rubric's interrater reliability, (c) describe how the development of BioTAP helped us create a faculty learning community, and (d) suggest how other departments and institutions can adapt BioTAP to suit their needs.