The purpose of this study was to assess the development and changes in preservice science teachers' subject matter and pedagogy knowledge structures as they proceeded through a professional teacher education program. Twelve secondary preservice science teachers were asked to create representations of their subject matter and pedagogy knowledge structures periodically (four times spanning the entirety of their subject-specific teacher education program) and participate in a videotaped interview concerning the eight knowledge structure representations immediately following student teaching. Qualitative analyses of knowledge structure representations and transcribed interviews within and between subjects were performed by one of the researchers and “blindly” corroborated by the other two researchers. Initial knowledge structure representations were typically linear and lacked coherence. Both types of knowledge structure representations were highly susceptible to change as a consequence of the act of teaching. Although there was some overlap between subject matter and pedagogy knowledge structures, they were reported to exert separate influences on classroom practice, with the pedagogy knowledge structure having primary influence on instructional decisions. Furthermore, the complexity of one's subject matter structure appeared to be a critical factor in determining whether the structure directly influences classroom practice.