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The study reports on the cause of misconceptions in physics have not been done in a major area. The source of misconceptions are students, teachers and learning resources while misconceptions are often caused by preconception, reasoning, intuition and associative thinking. This study aimed to find other factors affecting misconceptions that lead to students- alternative conceptions in learning physics, especially in kinetic theory of gases. The identification of factors affecting that influence students- misconception was conducted by using a set of responses in the questionnaires and administrated to 16 teachers and 66 students from six senior high schools in Surakarta. Interview to six teachers and twelve students as representatives was also held to support the data from questionnaire result. Misconceptions score were collected from the kinetic theory of gases test to explore students- alternative conceptions in learning physics. Two genuine factors affecting the cause of misconceptions were identified namely interpersonal skills and generic science skills.