The study examines biology, chemistry and pre-service science teachers’ ideas about the same concepts used in different courses such as biology and chemistry. Firstly, a pilot study was conducted to reveal what kind of different ideas were constructed by the students. Then, a questionnaire consisted of five open-ended questions was prepared, and administered to 152 students. Additionally, semi-constructed interviews were made with nine students to get more detailed information about the conceptions. As a result, it was revealed that students constructed different meanings from the same concepts such as organic and inorganic substance, reduction and oxidation, aim of evaporation used in biology and chemistry classes. In the last section of the study, the reasons why students constructed different meanings from the same concepts used in different courses were analysed. Finally, recommendations were noted to overcome those complications.