A geographic information system (GIS) can be a valuable research tool, helping scientists understand location and bridge the gaps between subjects in interdisciplinary research (IDR), which has been promoted for its real-world solutions. However, a GIS can be difficult to use and may require understanding of a number of concepts as well as tools and technology. This complexity is compounded by additional challenges commonly encountered in IDR. This paper examines some of the challenges facing learners of GIS in IDR projects, with a particular focus on the appropriateness of current teaching methods in this context.