Natural history museums (NHM) are important for students' learning and motivation. However, the lack or scarcity of NHMs in countries with emerging markets may hamper the learning process. Virtual 3D models represent an important tool to counterbalance the lack of access of students to NHMs. Our study aims to understand if the use of 3D models may help in the motivation and learning of zoology. The study comprised three groups: (1) "control" group, where the participants only received classes of "frontal teaching;" (2) "practice" group, where participants received, in addition to traditional classes, practical classes with biological material; (3) "3D model" group, where participants received the traditional class plus practical classes with 3D models of amphibian species. We used pre-questionnaires and post-questionnaires as an educational assessment method. Then we performed a two-way ANOVA test between the experimental groups. All three groups showed equivalent levels of motivation after the classes. Nevertheless, the "3D model" and "Practice" groups showed a significant (p < 0.001) increase in learning performance when compared to the "control" group, demonstrating the relevance of 3D models in the teaching of zoology especially in institutions distant from large biological collections.