This study endeavors to investigate the effectiveness of LearnM, an innovative augmented reality mobile application, in elevating the comprehension and assimilation of molecular structures among Grade 12 Science, Technology, Engineering, and Mathematics (STEM) students. LearnM showcases an immersive and interactive platform that empowers students to visualize and manipulate intricate three-dimensional models of molecular structures through the convenience of their smartphones. By integrating cutting-edge augmented reality technology, LearnM aims to transcend the traditional boundaries of textbook-based learning, fostering an engaging and dynamic learning experience. The research design employed in this investigation entails a quasi-experimental study with a pretest-posttest control group design. A cohort of 40 Grade 12 STEM students has been selected, with participants randomly assigned to either the experimental or control group. The experimental group will utilize the LearnM application, while the control group will receive conventional instruction. Pretest and posttest assessments will be administered to both groups, enabling a comprehensive analysis of the application’s impact on learning outcomes. The significance of this research lies in its potential to augment the body of knowledge within the realm of mobile learning and augmented reality, with a specific emphasis on molecular biology education. The integration of technology in education has become increasingly vital in the digital age, and this study endeavors to shed light on the effectiveness of such applications in enhancing students’ understanding of complex scientific concepts. Keywords: Augmented Reality, Mobile Application, Molecular Biology, STEM Education.