This study investigated pre-service science teachers' pedagogical content knowledge in the physics, chemistry, and biology topics. These topics were the light and sound, the physical and chemical changes, and reproduction, growth, and evolution. Qualitative research design was utilized. Data were collected from 33 pre-service science teachers (PSTs) by using open-ended questions. Data analysis was performed using descriptive analysis. The results indicated that some PCTs have sufficient information in terms of knowledge of learners in the above-mentioned topics. Ten PSTs mentioned that students have some misconceptions (e.g. light is a matter) in the light and sound. In the same way 17 PSTs stated that secondary school students have misconceptions (e.g. melting of was is a chemical change) in the chemistry topic. Also, seven participant wrote that students have misconceptions regarding biology topic (e.g. growth and evolution is the same). Moreover, some PSTs did not have sufficient information regarding instructional strategies and knowledge of assessment in these topics. Many of them stated that they use traditional instruction to overcome misconceptions on these topics. Likewise, many of them mentioned that they use open ended questions to determine these misconceptions. Implications for science teacher education are also presented.