Students? misconceptions in science can lead to a range of learning difficulties if the teacher does not choose the appropriate teaching strategies to reduce their frequency. In this paper, 13?14-year-old students? misconceptions regarding structure and states of matter, pure substances, and mixtures are explored. The teaching strategy with E-learning material was applied to examine its effects on the frequency of misconceptions. The research was conducted in urban schools in Bosnia and Herzegovina with 7th- and 8th-grade students. Findings pointed to the misconceptions originating in transferring the macroscopic observations into the submicroscopic level and in misinterpretation of the size of particles. Students who used E-learning material at school mostly had lower percentages of misconceptions in comparison to students from the control group and students who accessed the same E-learning material from their home. This indicates that the E-learning strategy could have promising results if applied more extensively at schools. This study aims to direct teachers? attention toward applying E-learning in chemistry teaching, for students to gain scientifically accepted knowledge and to reduce the occurrence of misconceptions.