The subject of molecular structures is one of the most important and complex subject in chemistry which a majority of the undergraduate students have difficulties to understand its concepts and characteristics correctly. To comprehend the molecular structures and their characteristics the students need to understand related subjects such as Lewis dot structures, molecular geometry, bond polarity, molecular polarity, resonance and hybridization. This study investigated the conceptual understanding levels and misconceptions held by university students about molecular structures subject. The sample of the study comprised of 88 undergraduate students enrolled in the Department of Mathematics and Science Education, Faculty of Education, Turkey. The participants responded to open-ended and interview questions regarding the subject. Students' responses were analyzed and their conceptual understanding levels were determined. The results indicated that students had lack of knowledge and misconceptions about the subject although they studied it in the university. Especially, they had poor knowledge about the molecular geometry, molecular polarity, resonance, and hybridization in molecular structures except for Lewis dot structures of molecules. Accordingly, implications have been made for more effective teaching approaches to ensure better understanding of the subjects.