Students commonly develop alternative ideas about topics in science. According to constructivist view of learning, students' alternative conceptions and misconceptions about the process of developing new knowledge should be highlighted. Remedy can be undertaken through conceptual change approach. In order to understand what factors causes 9th grade students to make mistakes in various sub concepts of shape of molecule, qualitative research design was followed. Misconceptions of the students about shape of the molecule were identified and analyzed. Accordingly, plan of action was framed for tackling each of the hard spots found among students. Lack of content information, previous knowledge, instructional approaches, process of assessment, cognitive and meta-cognitive strategies were attributed towards the cause of misconceptions.