The Conceptual Change Model (CCM) is an instructional approach that helps students learn by deliberately targeting their misconceptions. The teaching of such paleontological topics as evolution, phylogenetics, and functional morphology—three concept-rich units that are components of any paleontology course—is confounded by ingrained misunderstandings. The inquiry-based CCM was developed to take into account current theories of brain function. It fully supports the National Research Council's standards for inquiry and follows their recommendations for teaching science. The CCM instructional process allows students to: identify their own preconceptions, recognize the wide variety of beliefs held by classmates, confront their misconceptions, revise and reconstruct their ideas, apply their knowledge, and, finally, ask new questions for further study and growth. Implementation of the model provides a socially safe and challenging environment that engages students in ways not possible in traditional lecture settings. The CCM is employed in the upper-division course in paleontology at Florida Gulf Coast University. The principles of the paleontology course supports our marine science, environmental studies, and biology undergraduate programs. At the introduction of each topical unit, a short inquiry-based exercise is implemented both to reveal preconceptions carried by the students and to demonstrate the inconsistencies and problems with those conceptions. This then provides an opportunity to cleanly present the correct rendition of the concept.