In order for students to reach a level of meaningful understanding of chemistry, it is vital that they are able to form accurate relationships between different concepts. In particular, in organic chemistry, identifying intermolecular reactions, considering these reactions as a whole, and defining their results will make important contributions to attaining meaningful understanding. This study aims to explore how pre-service chemistry teachers identify aromatic compound reactions and form associations between them and to discover what kinds of learning difficulties they encounter in forming these associations. In this context, the study, conducted as phenomenographical research, was carried out at a faculty of education in Turkey with 15 pre-service teachers enrolled in the Department of Chemistry Education who had taken the Organic Chemistry 1 and 2 courses. Selected on the basis of purposive sampling, the pre-service chemistry teachers were first asked systemic assessment questions (SAQs) related to aromatic compound reactions. In these questions, the pre-service chemistry teachers were asked to identify 7 molecules in the class of aromatic compounds and complete a diagram by taking into consideration synthesis and reaction conditions. The pre-service chemistry teachers were also asked to indicate two reactions that were not included in the SAQs diagram, together with their reagents and conditions. After completing their responses to the SAQs diagram, individual interviews were held with each of the pre-service chemistry teachers using the think-aloud technique. The research revealed at the end of the quantitative analysis of the data obtained from the SAQs diagram that most of the pre-service chemistry teachers achieved moderate-level scores. At the same time, the qualitative analysis of the data obtained from the SAQs diagram and from the interviews showed that the pre-service chemistry teachers were more successful in identifying and forming associations with the reactions of “nitration” and “sulfonation of aromatic compounds” but had difficulty with the “Friedel–Crafts alkylation,” “oxidation” and “reduction” reactions and with the “bromination of alkenylbenzenes” and the “addition reaction of the double bond of alkenylbenzenes.” Another important finding resulting from this study was that only a few pre-service chemistry teachers were able to identify a new reaction on the SAQs diagram. All of these findings indicate that the pre-service teachers are not very equipped to form meaningful relationships in the context of aromatic compounds, which is one of the basic topics of organic chemistry.