Concept mapping activities were trialed over a 2 year period as part of an undergraduate microbiology course. This paper describes this developmental process and offers insight into the most beneficial ways of employing this tool in a higher education setting. The aim was to investigate the use of mapping activities to improve students' integration of the material presented and as a method of course evaluation. It was found that the emphasis placed on concepts at the beginning of the course had a profound influence on the trajectory of conceptual development exhibited by students. Once established, initial conceptual structures seemed resistant to change and restricted the subsequent choice of superordinate concepts. The approach was modified in the second year. Students were encouraged to restructure their understanding by producing a concept map as part of a collaborative group. The concept labels were prescribed and excluded the terminology that had appeared to constrain conceptual development in the previous year. Findings suggest that in order to optimize concept mapping activities they should: (1) reflect a student-centred teaching philosophy; (2) be collaborative; (3) be given sufficient time for reflection and development; (4) avoid using specific terms that restrict conceptual development by hindering appropriate switching between opposing conceptual frameworks. Linking the mapping activity to course grades provided an extrinsic motivation for active engagement in the task.