We know that most traditional approaches used in teaching of chemistry focus on macroscopic and symbolic levels of chemistry; for example, balanced chemical equations, mathematical calculations, graphical analysis, etc., and tend to ignore the microscopic level (Kelly et al., 2004). Naturally, instruction based on macroscopic properties and symbolic representations is also helpful for students in understanding of chemistry concepts, but such an instruction have some problems because students cannot see the nature and movement of atoms and molecules. In addition, teachers tend to ignore students’ alternative conceptions in traditional teaching approaches. On the other hand, CCT-CA instruction not only considers the students’ alternative conceptions, but also helps students to see microscopic world via computer animations. Based on the thesis of the dual-coding theory Kelly et al. (2004), state that better recall of pictures can be expected because they are coded both visually and verbally; and, if one mental representation is lost, the other is still available. Moving from this idea, we tried to combine CCT which predominantly consisted of verbal explanations with CA which included a series of visual images displayed in rapid succession on a computer screen. The combination of these methods was used in the study and became successful for students’ understanding of the underlined concepts. Therefore, we believe that the results of the study are different from the others and useful for future researches. On the other hand, some of the alternative conceptions are still encountered after the implementation. This indicates that CCT-CA instruction also has failed to alter some students’ alternative conceptions towards scientific ones, totally. For this reason, CCT-CA instruction also needs to be integrated with some other contemporary teaching methods to be more effective in enhancing students’ learning of chemistry concepts. In conclusion, we suggest that combining the methods of CCT and CA may be a useful way for teaching chemical bonding, and teachers may use this or another combination when teaching chemistry concepts. Undoubtedly, researchers may also improve our approach by integrating new teaching methods into this cooperation.