This study investigated Indonesian and Japanese students' understandings of macroscopic and submicroscopic levels of representing matter and its changes and the difficulties they have with these concepts. A multiple-choice questionnaire was constructed and delivered to 447 Indonesian and 446 Japanese public senior high school students. The data were analyzed using quantitative and qualitative methods. The findings of the study show students' understandings of macro- and submicroscopic levels are stronger for higher-grade levels, except that the Indonesian students' pattern is slightly different. The average percentage of students responding correctly on the macroscopic level ranges between 62% and 69% (Indonesia) and between 58% and 73% (Japanese), whereas on the submicroscopic level ranges between 56% and 62% (Indonesian) and 44% and 66% (Japanese). Their understandings of the macroscopic level, however, are higher than for the submicroscopic level. The soundness of students' understandings of the concepts increases with grade level, except for Indonesian pattern slightly different. The average percentage of students responding correctly ranges between 37% and 48% (Indonesian) and between 28% and 52% (Japanese). Furthermore, students' level of sound understandings of the concepts is lower than their understandings on either the macroscopic level or the submicroscopic level. It is found that students have great difficulties with and hold some alternative conceptions of the concepts of homogeneous mixtures, phase changes from solid to liquid, and phase changes from solid to gas. The study has implications, for example, the use of several routes to meaningful learning and the careful use of technical words.