Citrus depressa Hayata is the native and widespread citrus species in Taiwan. The notable character is that C. depressa has a distinct aroma different from local citrus. The ex situ germplasm of scions from different collection regions has variant leaf shapes and different odor characteristics. Establishing volatile biomarkers for classifying the local C. depressa is beneficial to commercial development. Volatile organic compounds (VOCs) of fresh leaves from seven C. depressa accessions which were collected from different locations in Taiwan were extracted by headspace solid-phase microextraction and analyzed by GC-MS. The volatile compositions from each season showed the diversity, and linalool, of which the average relative content is 52.7%, was the most volatile component in any season. The other main VOCs of leaves of C. depressa were γ-terpinene, limonene, β-ocimene, and α-terpineol. The result of linear discriminant analysis by VOC markers shows that there are two main different types which are (1) accessions from the central and the east of Taiwan and (2) accessions which are closer to C. depressa in Okinawa, Japan. Five major VOC-related synthase genes were selected and the gene expression was used to classify the varieties. The clustering result is the same with VOC-based discrimination. Our results reveal leaf volatile profiling is capable of being the discrimination markers, and the possibility for constructing molecular markers is directly related to characteristics from secondary metabolites phenotyping.