Metaphors play a central role in our language. Likewise, they are ubiquitous in the language related to imperceptible concepts including many chemical concepts. The present systematic review investigates what metaphorical mappings chemistry education research has examined. Specifically, we distinguish between instructional analogies designed for learning and domain-inherent metaphors present in chemical discourse. We pose the research questions: (i) what types of metaphorical mappings are present in chemistry education research and (ii) what the main findings of this research are. We find that instructional analogies are the focus of most research on metaphorical mappings with a special emphasis on two target concepts: atomic structure and chemical reactivity. Most analogies aimed to either make these concepts more tangible or to relate them to the specific lived experience of the students. Research on domain-inherent metaphors is limited to the analysis of conceptual metaphors that experts or students employ during problem-solving and textbook analyses, all related to entropy. We conclude that the source domain needs to be accessible to the learner and that they need to be aware of the limitations. One way to ensure that is by introducing multiple analogies. However, given the gaps we uncovered in this review, we recommend that future research should focus on a more comprehensive analysis of metaphorical mappings inherent to chemical discourse and their impact on learning processes.