One of the key agendas for the emerging field of disciplinary-based education research is the evaluation of the trajectory of disciplinary knowledge development from novice to expert. However, with the ongoing promotion of student-centered and collaborative undergraduate science classrooms, it is unknown how peer discourse during these exercises might influence (promote or hinder) student construction of expert knowledge. This study documented the knowledge structures of n = 13 undergraduate biology students in a first semester biology course for majors across four instructional units. Participants constructed both individual and group-negotiated concept maps and map complexity, propositional stream similarity, and propositional accuracy were used as measures of quality of knowledge structure. Results indicated that on individually-constructed maps, in general, students had moderate quality knowledge structures when compared to experts. Individual map complexity seemed to increase over time, but stream similarity and propositional accuracy were more dependent on content unit. Group-constructed maps were consistently more accurate than individually-constructed maps. Results are discussed in the context of the use of collaborative concept mapping as a means to develop disciplinary expertise in biology.