Microorganisms is a Year 6 Science subject that primary school students find considerably less attractive because of the enormous facts that require them to have good imaginary skills to understand. Only limited applications are available on smartphones as tools to learn subjects, especially Science, Technology, Engineering and Mathematics (STEM). Since the young generation is very much into current technology, there is a need to develop an application to gain students' interest and improve their understanding of microorganisms. Therefore, a microorganism learning application that combines augmented reality (AR) and gamification called Microorganisms was developed. The Microorganisms prototype includes two modules; learning and training. The learning modules use AR technology that scan marker images to display a digital layer of microorganisms in three dimensions (3D). Meanwhile, the training module is represented through gamification consisting of quiz questions, a timer, and a score. The application was designed using Agile methodology and developed using various software such as Unity, Autodesk 3ds Max, Vuforia, and Firebase. Ten respondents, nine students and one teacher in a primary school, assessed the prototype through experimental testing. The results showed that, on average, the user satisfaction value was 4.6 out of 5. Thus, the Microorganisms application based on AR and gamification can be considered a good learning tool for primary school students to learn about micro-organisms.