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Over the past few decades, researchers have focused on the lack of conceptual understanding of mole concept because it is considered to be difficult for students globally. Due to its abstract and mathematical nature, chemistry teachers tend to use algorithmic teaching strategies to provide learning experiences for students, resulting in superficial understanding of the concept. Past researchers have focused more on teaching strategies and learning experiences in the classroom for the topic but relatively less on students’ mental processes. The knowledge embedded in the mind of learners is the result of the learning experiences they are subjected to by their teachers. The objective of this study is to investigate how knowledge on mole concept is organised in the brain of learners using the Connectivity Model of Semantic Processing (CMSP). This theory explains that knowledge is structured in the form of memory networks in the brain, either in the form of hierarchical memory network (HMN) or interconnected memory network (IMN). The mind maps generated by research participants on this concept were analysed based on CMSP as the representation of their memory networks. Then it was compared with their learning experiences in the classroom. The findings show that those who had IMN were able to inter-relate concepts as they were given more emphasis on thinking process during the lesson and the concepts were taught simultaneously. On the contrary, those who learnt one concept after another, separately, had HMN and were not able to relate concepts.