Research on animals is one of the most controversial ethical issues in our society. It is imperative that animal welfare is being considered and the harm and distress to animals used in research is minimized. This could be achieved through implementation of the so-called 3Rs principles for animal research, which are now implemented in many legislations worldwide. These principles serve as a basis for research without the use of animals (Replacement), with as few animals as possible (Reduction), and in which the animal’s welfare is as good as possible (Refinement). While there has been a lot of focus on implementation of these principles, only a few studies have documented the knowledge and adoption of the 3Rs among researchers. One field that has been particularly neglected is ecological research, which can involve many practices that affect animal welfare. Moreover, the knowledge, experience, and attitudes about animal use in ecological research and education has never been examined before. In order to close this gap, I conducted a survey among European ecologists. Responses from 107 respondents from 23 countries revealed that lethal and invasive research methods are prevalent, and that more than half of the respondents have never heard of the 3Rs principles for animal research. Major concerns are also the lack of calculation of the minimum sample size and widespread of dissection classes as part of education. Additionally, most respondents experienced ethical doubts about their research, and did not receive any training in animal welfare or ethics. These findings revealed that it is necessary to implement rigorous standards for ecological research and enforce the implementation of the 3Rs principles. Furthermore, the evaluation of current educational practices in ecology is urgently needed.