Metabolite fingerprinting of bokbunja (Rubus coreanus Miquel) using LC-MS according to the cultivation region and the maturity level was performed. The endogenous metabolites were extracted with 80% cold ethanol and the total content of phenolics and anthocyanins compounds was assessed. Accurate mass fingerprinting with chromatographic separation successfully classified bokbunja based on the metabolite profile. Unsupervised classification method (PCA) and supervised prediction model (OPLS-DA) provided good capability in categorizing the samples according to the region and the maturity level. Additional tandem-mass spectrometry analysis allowed the identification of some anthocyanin derivatives that showed the most dramatic increase during ripening period (e.g., cyanidin-3-O-glucoside and cyanidin-3-O-rutinoside).