There is a close relationship between chemistry and physics in the context of atomic structure, which is usually covered in both courses at the secondary-school level. However, little emphasis has been put on determining whether the students developed correct understanding of the quantum structure when they studied it in both the courses. The purpose of this study was to reveal - by using the concept mapping tool - the cognitive structures used by twelfth-grade students to understand atomic structure. One hundred forty-five students from three secondary schools in Ankara, Turkey participated in the study. The qualitative content analysis technique was employed to analyse concepts, levels of connection, and linking phrases in students' concept maps drawn for the atom. The analysis results revealed that the students had a limited understanding of the quantum structure of the atom, even after studying the topic in chemistry and physics courses. They relied on classical ideas to understand atomic structure. The results suggest that concepts related to atomic structure should be appropriately used not only within a particular subject (e.g. physics) but also across the two subjects to help students understand the scientifically correct atomic structure. Further, several other implications for secondary-school science teaching are discussed.