Spatial understanding of molecules in molecular biology provides a better understanding of molecules in isolation and relation to their next elements. Augmented reality (AR) has recently been developed as a computer interface that enables the users to see the real world with virtual objects superimposed on it. We report a method that shows the use of AR and data provided from protein data bank (PDB) to facilitate the teaching of macromolecules in biology. Users can easily convert the molecules structures obtained from PDB to a 3D format and use it with an AR application to study the molecules from different perspectives. A sample of 60 college students was assigned randomly to one of two conditions namely 2D and AR. At the end of the experiment, participants completed a comprehensive test and then a satisfaction questionnaire. The results of the study showed a significant difference between 2D and AR in satisfaction, the media usability, perception, and apprehension.