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This study mainly examines the effects of computer-aided individual and collaborative argument mapping practices on pre-service science teachers’ reasoning abilities by adopting an experimental research method, i.e., pre-test post-test control group pattern. Fifty senior pre-service science teachers participated in this study. The science writing heuristic tool and individual argument mapping practices were used within the scope of the subject of optics for eight weeks in the experimental and control groups. In addition, students in the experimental group participated in collaborative argument mapping practices. The logical thinking ability test was used as a data collection tool. Results of the quantitative analysis showed that the pre-service teachers who participated in collaborative argument mapping practices were more successful in developing their reasoning skills. In this regard, computer-assisted collaborative argument mapping is an effective method for improving reasoning skills. These findings can be attributed to the fact that collaborative argument mapping gives students more room for group discussion in the context of the subject. It is possible to say that collaborative argument mapping includes social and cognitive activities required for the development of reasoning skills. In other words, in collaborative argument mapping, the pre-service teachers with different views in the same group had the opportunity to develop their reasoning skills by critically questioning their own ideas and those of their group mates. In general, it is normal for collaborative pre-service teachers who have more social and cognitive argumentation experiences to perform better in terms of reasoning than the individual argument mapping group.