There exists bias among students that learning organic chemistry topics requires rote learning. In this paper, we address such bias through an organic chemistry activity designed to promote argumentation. We investigated how pre-service science teachers engage in an argumentation about conformational analysis. Analysis of the outcomes concentrated on (a) pre-service teachers' understanding of conformations of alkanes (b) the nature of the pre-service teachers' discourse; (c) the quality of pre-service teachers' argumentation; and (d) pre-service teachers' spatial ability. Various measures were used to trace (a) conceptual understanding through the answers in the writing frames, (b) the nature of the pre-service teachers' discourse using two different codes, (c) the quality of pre-service teachers' argumentation by counting the number of episodes with higher-level argumentation, and (d) spatial ability by Spatial Ability Test. The results showed that high performing groups had multiple rebuttals in their argumentation and low performing groups had problems in evaluating the credibility of evidence. Furthermore, we observed that spatial abilities play an important role in pre-service teachers' engagement in argumentation. The findings help understanding of how to further enhance pre-service teachers' conceptual understanding and engagement in argumentation regarding organic chemistry concepts.