The early detection of tree health pests and disease is an important component of biosecurity to protect the aesthetic, recreational and economic importance of trees, woodlands and forestry. Citizen science is valuable in supporting the early detection of tree pests and diseases. Different stakeholders (government, business, society and individual) will vary in their opinion of the balance between costs and benefits of early detection and consequent management, partly because many costs are local whereas benefits are felt at larger scales. This can create clashes in motivations of those involved in citizen science, thus leading to ethical dilemmas about what is good and responsible conduct for the use of citizen science. We draw on our experience of tree health citizen science to exemplify five dilemmas. These dilemmas arise because: the consequences of detection may locally be severe (e.g. the destruction of trees); knowledge of these impacts could lead to refusal to make citizen science reports; citizen science reports can be made freely, but can be costly to respond to; participants may expect solutions even if these are not possible; and early detection is (by definition) a rare event. Effective engagement and dialogue across stakeholders, including public stakeholders, is important to properly address these issues. This is vital to ensure the public’s long-term support for and trust in the use of citizen science for the early detection of tree pests and diseases.