The purpose of the study is to investigate the effect of cooperative and individual learning methods on the conceptual understanding at sub-micro level of pre-service science teachers (PST) in equilibrium chemistry. The study was conducted on 52 PSTs. A pre-test/posttest non-equivalent quasi-experimental design was used in this study. Data collection instruments used as pre- and posttest as a Module Test (MT) consisted of seven open-ended questions developed by the researchers. Although, participants were identified with a convenience sampling method, each group were randomly assigned. For this reason, three study groups were selected, and each implementation was randomly assigned. Groups was determined as Cooperative Student Teams-Achievement Divisions (STAD, E1) and Reading-Writing-Application (RWA, E2) methods, and Individual Learning (IL, E3) method. The data gathered with the MT were evaluated using content analysis. According to findings, there was not a significance difference among groups related to conceptual understandings at equilibrium chemistry. However, some misconceptions related to topic were decreased. Consequently, when three learning methods are used that it is more likely to misconceptions of the PSTs will be treated, while at the same time micro level understanding will improve.