For proper understanding of science concepts their simultaneous representation at all three levels, i.e. the macroscopic, the sub-microscopic and the symbolic levels is required. The research results show that learners have difficulties in clarifying the concepts, phenomena and processes at the level of particles at all levels of schooling due to the abstractness of science concepts. The key to a better understanding of science concepts is their representation on real life cases that are close to learners. The purpose of the research presented in this paper is to show the manner in which the learners explain the particle nature of the aggregate state of the substance. The qualitative study included five students from 7th and 9th grade of elementary school, and five students from the 1st year of gimnazija. For data collection a semi-structured interview with four authentic problem tasks was used. The research results show that all respondents correctly identify the aggregate states of matter at the level of particles, but they have difficulties in justifying their decisions. The study confirmed the existence of misunderstanding with regard to: (1) the interpretation of the particle nature of matter, (2) non-discrimination between the particles and matter, and (3) description of the sub-microscopic levels of matter with a macroscopic level. The research findings are consistent with the findings of other studies and provide teachers with insights into the contemplations of learners. These findings can be used by teachers in the classroom to achieve better understanding of science concepts.