This study investigated pre-service chemistry teachers' pedagogical content knowledge of the nature of science (NOS) in the content of the particle nature of matter. Qualitative research design was utilized. Data were collected from seven pre-service chemistry teachers (PCTs) by using open-ended questions, interviews, observations, lesson plans, and reflection papers. The results indicated that while most of the PCTs showed improvement in terms of understanding of the target aspects of NOS, knowledge of learners and instructional strategies, the majority of PCTs did not make progress regarding knowledge of assessment during the study. Implications for science teacher education are also presented. (Contains 5 tables.)