The aim of this study is to comparatively investigate the effects of hands-on models (HMs) and computer simulations (CSs) on teaching the phases and eclipses of the Moon. In this study, two different HMs were developed, and three different CSs were used. The research work group consisted of 100 pre-service science teachers. A quasi-experimental method with two groups (teaching through hands-on models [THM] and teaching through computer simulations [TCS]) was used in this study. The data for the study were obtained by using an open-ended questionnaire form. The data were acquired three times as pre-instruction, post-instruction, and long-after instruction (retention) and were analyzed through a content analysis technique. The analyses were implemented in two stages (i.e., a question-by-question analysis and an integrated analysis) by evaluating the answers given to all questions together. As a result of the analyses, it was determined that both methods are effective in teaching the phases and eclipses of the Moon. However, when the retention data were examined, it was observed that more students in THM group answered correctly than TCS group. Besides, upon the integrated analysis, it was concluded that THM, as opposed to TCS, led more pre-service teachers to the "scientific" model. From this point of view, it has been proposed to popularize the usage and production of HMs in astronomy education. Finally, the conditions that must be taken into account in order to overcome some alternative thoughts identified in the phases and eclipses of the Moon are noted.