This study explored the perceptions of ethical issues in supervision among doctoral students and supervisors. The nature of ethical issues identified by doctoral students (n = 28) and their supervisors (n = 14) is explored and the degree of fit and misfit between their perceptions in two cases representing the natural and behavioural sciences is analysed. Supervisors and students identified different ethical issues, which suggest that there are aspects in the supervisory relationship about which there is no shared understanding. There were also differences between the ethical issues emphasised in the natural sciences from those emphasised in the behavioural sciences, suggesting differences between the domains.