Understanding complex systems is fundamental to understanding science. The complexity of such systems makes them very difficult to understand because they are composed of multiple interrelated levels that interact in dynamic ways. The goal of this study was to understand how experts and novices differed in their understanding of two complex systems, the human respiratory system and an aquarium ecosystem. In particular, we examined how a representation of complex systems, Structure-Behavior-Function theory (SBF), might account for these differences. SBF is particularly relevant in understanding biological systems because an important domain principle is the relation between form, function, and mechanism. Our results demonstrated that there were minimal differences between the expert and novice groups on structures, but that the locus of the difference was on understanding causal behaviors and functions, the least salient elements of the systems. Mental model analysis provided largely convergent results. We also found differences between the two different kinds of experts in each domain. These results suggest that SBF does capture expert-novice differences and may have implications for instruction.