Studying complex systems is increasingly important in many science domains. Many features of complex systems make it difficult for students to develop deep understanding. Our previous research indicated that a function-centered conceptual representation is part of the disciplinary toolbox of biologists, suggesting that it is an appropriate representation to help students develop deep understanding. This article reports on the results of two experiments that investigate how hypermedia using a conceptual representation influences pre-service teachers' and middle school students' learning of a complex biological system, the human respiratory system. We designed two versions of instructional hypermedia based on the structure-behavior-function conceptual representation. One hypermedia was function-centered which emphasized the function and behavior of the system, whereas the other was focused on the structure of the system. We contrasted the instructional effectiveness of these two alternative conceptual representations. The results of both studies indicated that participants using the function-centered hypermedia developed deeper understanding than those using the structure-centered version. This proof-of-concept study suggests that the function-centered conceptual representation is a powerful way to promote complex systems understanding. (Contains 4 tables, 4 figures, and 2 notes.)