Typing techniques are laboratory methods used in outbreak management to investigate the degree to which microbes found within an outbreak are related. Knowledge about relational patterns between microbes benefits outbreak management, but inevitably also tells us something about the relational patterns of the people hosting them. Since the technique is often used without explicit consent of all individuals involved, this may raise ethical questions. The aim of this study was to unravel the complex ethical deliberation of professionals over the use of such techniques. We organised group discussions (n = 3) with Dutch outbreak managers (n = 23). The topic list was based on previously identified ethical issues and discussions were analysed for recurrent themes. We found that outbreak managers first and foremost reflect on the balance of individual harm with public health benefit. This key question was approached by way of discussing four more specific ethical themes: (1) justification of governmental intervention, (2) responsibility to prevent infections, (3) scientific uncertainty and (4) legal consequences. The themes found in this study, rephrased into accessible questions, represent the shared ethical understanding of professionals and can help to articulate the ethical dimensions of using molecular science in response to infectious disease outbreaks.