Gas chromatography coupled with mass spectrometry (GC-MS) was applied to analyze the essential oil extracted from the leaves of 50 individual plants of Cinnamomum camphora, which were collected from the same mountain in Jiangxi province of China. 32 peaks in total were identified in these samples, which were then categorized into five chemotypes (bornel type, BN; camphor type, CP; isoneolidol type, ID; cineole type, CE; linalool type, LN) according to the primary component in the essential oil. In the meanwhile, total DNA was extracted from each sample for random amplified polymorphic DNA (RAPD) analysis, As a result, a total of 97 amplification products derived from 10 RAPD primers were obtained. These RAPD data were then analyzed using SPSS 10.0 software with 1 and 0 matrix, Jaccard’s coefficient and between-group linkage methods. Our results revealed that the estimated Jaccard’s differences between chemotypes varied in the range of 0-25, and that the pattern obtained from RAPD was totally accordant with the identification of GC-MS and the biosynthesis pathways of terpene. Thus, we propose that both GC-MS and RAPD are reliable and useful to identify the chemotypes of Cinnamomum camphora, and that quality control and large-scale cultivation of Cinnamomum camphora are possible.