Students come across with the notion of atom almostevery year during their education life. Higher conceptual understandings ofatomic theories among science teachers is of crucial importance in theirunderstanding of physics and chemistry courses. In this sense, the purpose ofthe present study is to investigate which of the atomic theories scienceteachers often confuse and to discuss the possible reasons behind the confusionof one theory with the other. This study used the phenomenology method ofqualitative research. Participants of the study were comprised of 55 first andsecond year university students attending the Department of Science Teachingduring the 2015-2016 academic year. In order to discover the most confusingatomic theories and the reasons of this confusion, students were asked to writedown the atomic theories that they often confuse with one another and thereasons why they do so. Using content analysis, two independent coders analyzedthe collected data. The result of the analyses revealed that students mostlygot confused between Bohr’s Atomic Theory and Modern Atomic Theory. It was alsofound that the underlying reasons of this confusion were that “In both theory,the protons and neutrons are found together at the center of the atom (thenucleus) surrounded by electrons spinning around it” and “students cannotdifferentiate between the concepts of layer, orbit and shell”, and somerecommendations were offered concerning the instruction of these subjects.