Problem-based learning (PBL) is a protagonist of constructivism widely used successfully in higher education. PBL is a learner-centered instructional and curricular approach that can use real problems for the development of the teaching and learning process. On the other hand, the complexity of knowledge of Ecotoxicology, as well as the importance of this field for Environmental Health and society demand reflections and proposals for the training of professionals who work in this field. Therefore, in accordance with the principles of PBL, this strategy can effectively contribute to the training and professional practice of ecotoxicologists. We report herein the importance of the principles of PBL for the training of ecotoxicologists, including the discussion of a case study using fish biomarkers for the development of this teaching strategy. Teaching ecotoxicology through PBL principles allowed students to develop several advantages for Ecotoxicology training through the discussion of an authentic, real life problem that engaged them in its discussion, functioning as a stimulus for learning. The students were able to develop laboratory skills, group work competences, understand basic concepts and fundamentals of Ecotoxicology and become empowered regarding skills and competences for future practice.