The cubeb berry has been used as a spice and medicinal herb since medieval times. In China, Litsea cubeba (Lauraceae) has been designated as the cubeb tree; in other countries, Piper cubeba (Piperaceae) is considered as the cubeb. Since most cubeb berries in the Korean market are imported from China, there is a need to develop an efficient analytical method for the identification of the origin of cubeb fruit. Thirty-two commercial cubeb samples were collected from China, Korea, and Indonesia, and direct analysis in real time mass spectrometry (DART®-MS) was employed to obtain a chemical fingerprint of each sample for multivariate analysis. Cubebene was identified as a marker molecule for P. cubeba, and all cubeb samples from Korean markets were identified as the fruit of L. cubeba. DART®-MS fingerprinting together with principal component analysis can be applied as a promising method for rapid identification and/or quality control of cubeb berries.