Doctoral supervision involves the analysis of situations and decision making, some of which include ethical perspectives. This research endeavoured to gain a better understanding of the nature of the ethical problems encountered by supervisors. We have interviewed fourteen supervisors in two disciplines: the natural sciences and the behavioural sciences. We have identified the ethical issues in light of five ethical principles, namely respect for autonomy, non maleficence, beneficence, justice, and fidelity. We have located the ethical issues within the supervisory activity in two locations: the dyadic supervisor-student relationship and the academic community. The study shows that supervisors encounter a plethora of ethical issues. Many of the supervisors were highly aware of the ethical challenges in supervision and actively worked to anticipate and prevent ethical problems. The supervisors described a number of sustainable solutions, but at the same time, ethical problems and malpractice were reported. This suggests that the complexities of ethics are not always evident to the actors themselves. We claim that in order to expose and scrutinize supervision practices, it is insufficient to analyse the ethical issues only on dyadic level. What appears to boil down to a dyadic relationship may in fact be indicative of the values, attitudes, norms, and practices of the community.