The concepts of Natural Products Chemistry (NPC) is taught in a hierarchy of complex concepts into simple concepts, beginning of primary metabolites and secondary metabolites through synthesis of alkaloids. This study examines the understanding of the concept of students in the matter of primary metabolites and secondary metabolites. Total respondents involved in this study are 19 students majoring in chemistry education on semester eight from one of the state university of West Nusa Tenggara, Indonesia. All respondents had a previous NPC lectures in semester six. This research uses descriptive method with percentage analysis and statistical tests. Data obtained through the technique of CRI (Certainty Response Index) and the modified CRI. There are significant differences between the techniques of data from CRI and modified CRI. Taking into account the culture of students in Indonesia which is tended not sure of the answer given, so the discussion in this study use data from the modified CRI technique. The results showed 28.95% of students understand the concepts very well; 41.58% had misconceptions, and 29.47% did not know the concept. Misconceptions occur at all levels of learners, both of which have the capability of high, medium, or low.© 2012 IOJES. All rights reserved