The aim of the presented study is to identify a simple applicable method to distinguish between garlic clones that are used in pharmaceutical or food industry. Four different clones of garlic (Balady, EGA 3, EGA 4 and Growers clone) cultivated in Egypt were differentiated using morphological, cytogenetical, molecular and chemical characterization. Results of the morphological and cytogenetical characters analysis showed that there were considerable variations for all studied traits except for three; leaf width, stem diameter and chromosome numbers. Additionally, SSR (simple sequence repeats) and ISSR (inter simple sequence repeats) markers showed a high level of genetic variation among the four garlic clones. Moreover, Headspace Gas Chromatography and Mass Spectroscopy (HS GC-MS) was used for identifying and comparing the volatile constituents. The resulting peaks showed thirteen major constituents (prop-2-en-1-ol, 5-Hexenal, trans-2-trans-7-nonadiene, 1-propene,3,3`thiobis, 1-Propene, 3-(methylthio)-, disulfide,methyl-2-propenyl, camphene , disulfide, di-2-propenyl , Trisulfide, methyl-2-propenyl, Diallyltetrasulphide, 2-vinyl-[4H]-1,3-dithiin, Trisulfide, 1- Trisulfide, di-2-propenyl , 1,3Dithiane and Trisulfide, dimethyl ) were present in the four analyzed clones. The percentage of active volatile constituents in each clone could be used as chemical markers to distinguish between these clones. Accordingly, HSGS/MS is a considerably simple and fast method that can be used for initial identification of all four clones under the same conditions using the above compounds. The analysis can be performed on both entire fresh or powdered plant forms.