The move from learning science from representations to learning science with representations has many potential and undocumented complexities. This thematic analysis partially explores the trends of representational uses in science instruction, examining 80 research studies on diagram use in science. These studies, published during 2000-2014, were located through searches of journal databases and books. Open coding of the studies identified 13 themes, 6 of which were identified in at least 10% of the studies: eliciting mental models, classroom-based research, multimedia principles, teaching and learning strategies, representational competence, and student agency. A shift in emphasis on learning with rather than learning from representations was evident across the three 5-year intervals considered, mirroring a pedagogical shift from science instruction as transmission of information to constructivist approaches in which learners actively negotiate understanding and construct knowledge. The themes and topics in recent research highlight areas of active interest and reveal gaps that may prove fruitful for further research, including classroom-based studies, the role of prior knowledge, and the use of eye-tracking. The results of the research included in this thematic review of the 2000-2014 literature suggest that both interpreting and constructing representations can lead to better understanding of science concepts.