In this study we measured changes in science teachers' conceptual science understanding (content knowledge) and pedagogical content knowledge (PCK) while participating in a problem-based learning (PBL) model of professional development. Teachers participated in a two-week long workshop followed by nine monthly meetings during one academic year that focused on deepening their content understanding and their teaching practices. We analyzed teachers' short writings and concept map depictions of their understanding, and found teachers significantly developed components of pedagogical content knowledge and clinical reasoning, such as knowledge of assessment. Gains on conceptual understanding of science, however, were limited to one group of teachers. We conclude that this PBL approach to professional development advanced components of science teachers' strategic pedagogical content knowledge and discuss the ongoing challenges in measuring changes in teachers' understanding in the context of an evolving PBL model of professional development.