BackgroundModern instrumental analysis technology can provide various chemical data and information on tea samples. Unfortunately, it remains difficult to extract the useful information. We describe the use of chemical fingerprint similarities, combined with principal component and cluster analyses, to distinguish and recognize Pu-erh green teas, which from two tea mountains, Wuliang and Jingmai, in the Pu-erh district of Yunnan province. The volatile components of all 20 Pu-erh green teas (10 Wuliang and 10 Jingmai teas) were extracted and identified by headspace solid-phase micro extraction (HS-SPME) combined with gas chromatography-mass spectrometry (GC-MS).ResultsSixty-three volatiles (including alcohols, hydrocarbons, ketones, and aldehydes) were identified in the 20 Pu-erh green teas, and differences in compound compositions between them were also observed. Through fingerprint similarity, combined with principal component and cluster analyses, the 20 Pu-erh green teas were differentiated successfully based on their volatile characteristics.ConclusionsThis study demonstrates that the GC-MS combined with chemical fingerprint and unsupervised pattern recognition method is suitable for the investigation of the volatile profiling and evaluating the quality and authenticity of teas related to the different origins.Graphical abstractDifferentiate Pu-erh green teas from different tea mountains by using chemical fingerprint similarity and multivariate statistical methodsElectronic supplementary materialThe online version of this article (doi:10.1186/s13065-016-0159-y) contains supplementary material, which is available to authorized users.