Chemistry students' explanations of ionisation energy phenomena often involve a number of non-scientific or inappropriate ideas being used to form causality arguments. Research has attributed this to many science teachers using these ideas themselves (Tan and Taber, in "J Chem Educ" 86(5):623-629, 2009). This research extends this work by considering which atomic models are used in pre-service teachers' explanations and how that relates to the causality ideas expressed. Thirty-one pre-service teachers were interviewed. Each was asked to describe and explain four different atomic representations (Rutherford, Electron cloud micrograph, Bohr and Schrodinger types) in as much detail as they could. They also provided an explanation for the subsequent ionisation energy values for an oxygen atom and identified which representations were helpful in explaining the values. Significantly, when pre-service teachers only used Bohr type representations, they did not use repelling electron ideas in their explanations. However, arguments that were based on electron-electron repulsion used features from Schrodinger type atoms. These findings suggest that many pre-service teachers need to develop their atomic modelling skills so that they select and use models more expertly and that subsequent ionisation explanations offer a context in which to explore different atomic models' limitations and their deployment as explanatory resources.