This study aims to analyse prospective chemistry teachers' cognitive structure related to the subject of covalent and ionic bonding. Semi-structured interviews were conducted with the participants in order to determine their cognitive structure, and the interviews were audio recorded to prevent the loss of data. The data were transcribed and transferred into the computer medium. Furthermore, a flow map was prepared for each prospective chemistry teacher and then was analysed firstly in terms of quantitative variables used in presenting cognitive structure in quantitative statements. Secondly, the statements in the flow maps were analysed in terms of comprehension level. In consequence, it was found through flow maps that prospective chemistry teachers were not very different from each other in terms of cognitive structure and that their cognitive structures were full of inadequacies and misconceptions. Having analysed the statements in the flow maps in terms of the levels of comprehension, the scope and richness of prospective chemistry teachers' cognitive structures were exhibited in more details.