The crystal structure is an important topic in the STEM field and the basic knowledge to determine the material structure and its behaviour. There is a wealth of literature on three-dimensional (3D) and augmented reality (AR) technology to represent 3D crystal environments to provide a new way of visualisation and to foster spatial skills. This article aimed to develop and evaluate an AR system for teaching Bravais Crystals in Natural Science, especially the potential of AR as an innovative teaching tool to encourage spatial skills. The users were satisfied with the AR system (Mean = 4.3, SD = 0.49) to learn spatial representation techniques in a cooperative learning environment. The AR system provided excitement and motivation and was attractive and flexible while allowing the students to engage in independent learning.