A simple, fast, and accurate method was developed for the identification of the phytoconstituents in the methanolic extracts of stems and roots of Ephedra sinica and Ephedra beatona. The developed GC-MS study indicated that the phytochemicals: 1H-Quinolinone, 2-hexadecen-1-ol, 9-octadecenamide and 2-methyl-6-(5-methyl-2-thiazolin-2-ylamino) pyridine were found in the stems extracts in appreciable percent compositions. Stems extracts contain more constituents than roots extracts. It was surprisingly observed that all peaks in Ephedra beatona chromatograms match with those in Ephedra sinica chromatograms; (peak by peak matching) and the major constituents are also similar. The wide use of the two plants in the treatment of several types of cancer and as antidiabetics is the major driving force to study their chemical composition.