Background: Cyperus scariosus (CS) R.Br and Cyperus rotundus (CR) L. belongs to Cyperaceae family which is well-reputed in the traditional systems of medicine. Although they grow in different agro-climatic conditions, they are often considered to be synonymous with each other. Objective: The present study was aimed to systematically classify both the species CS and CR through their morphological features and chemical profiling using liquid chromatography-mass spectroscopy (LC-MS), gas chromatography-mass spectroscopy (GC-MS) and thin layer chromatography patterns of the rhizome extracts. Materials and Methods: A method (LC-MS analysis) has been developed on Agilent LC-MSD Trap SL mass spectrometer equipped with Waters HR C18 column (3.9 mm × 300 mm, 6 μm) using isocratic elution with acetonitrile and water (70:30% v/v ratio). GC-MS analysis was performed on a Shimadzu GC-MS-QP 2010 equipped with DB-5 capillary column (30 m × 0.25 mm × 0.25 μm). Results: Chemoprofiling of CS and CR using LC-MS and GC-MS suggested that these two are different based on their deferential spectral pattern, however, some of the common peaks were found in both the species. In addition, we also performed the preliminary phytochemical investigation of hexane and chloroform extracts of these species, which led to the isolation of stigmasterol, β-sitosterol and lupeol as major constituents in CS. Conclusion: In summary, we have developed optimal chromatographic conditions (LC-MS and GC-MS) and morphological profiles to classify both the species, that is, CS and CR. Collectively, our analytical results coupled with the morphological data clearly suggested that CS and CR are morphologically different.