This study focused on exploring students' and supervisors' perceptions of ethical problems in doctoral supervision in the natural sciences. Fifteen supervisors and doctoral students in one research community in the natural sciences were interviewed about their practices and experiences in the doctoral process and supervision. We explored to what extent doctoral students and supervisors experienced similar or different ethical challenges in the supervisory relationship and analyzed how the experiences of ethical dilemmas in supervision could be understood in light of the structure and practices of natural science research groups. The data were analyzed by theory-driven content analysis. Five ethical principles, namely non-maleficence, beneficence, autonomy, fidelity and justice, were used as a framework for identifying ethical issues. The results show that one major question that appears to underpin many of the emerging ethical issues is that the supervisors and students have different expectations of the supervisory role. The second important observation is that doctoral students primarily described their own experiences, whereas the supervisors described their activities as embedded in a system and elaborated on the causes and consequences at a system level.