Among three levels of chemical representation, the sub-microscopic level is the most difficult to learn by students. To solve the problem, it is assumed that the concept of the discontinuous nature of matter or particle concept should be mastered initially by students before they learn sub-microscopic representations of further chemical phenomena. 131 junior high school students from two schools participated in this study. The study was carried out by implementing structure-oriented chemistry teaching on the particle concept that was assisted by the courseware and was continued by teaching the changing state of matter. The research instruments were written tests, questionnaire, observation sheet and interview guideline. Research data were collected before and after the use of the courseware, as well as before and after the teaching of the changing states of matter. The results show that the use of the courseware increases students' understanding of the particle concept for both male and female groups. Meanwhile, particle concept only affects the students' understanding of sub-microscopic representations of the changing states of matter in general and based on gender.