Engineering education, like many fields, has started to explore the benefits of concept maps as an assessment technique for knowledge integration. Because they allow students to graphically link topics and represent complex interconnections among diverse concepts, we argue that concept maps are particularly appropriate for assessing interdisciplinary knowledge integration. The results from a year-long study of a design course in green engineering demonstrate the viability of this approach. However, this research also highlights important issues in faculty scoring of interdisciplinary concept maps that may not be present when maps are used in traditional single-discipline settings. The interdisciplinary setting revealed differences in (1) evaluation criteria, (2) expertise, and (3) investment. We conclude with suggestions for selecting and training scorers to address these issues.