Models and modelling are key tools for scientists, science teachers and science learners. In this paper we argue that classroom-based research evidence demonstrates that the use of models and analogies within the pedagogy of science education may provide a route for students to gain some understanding of the nature of science. A common theme to emerge from the literature reviewed here is that in order to successfully develop conceptual understandings in science, learners need to be able to reflect on and discuss their understandings of scientific concepts as they are developing them. Pedagogies that involve various types of modelling are most effective when students are able to construct and critique their own and scientists' models. Research also suggests that group work and peer discussion are important ways of enhancing students' cognitive and metacognitive thinking skills. Further we argue that an understanding of science models and the modelling process enables students to develop a metacognitive awareness of knowledge development within the science community, as well as providing the tools to reflect on their own scientific understanding.