Ten Fagonia species grown in the Libyan Desert subjected in this study. The study focused on both micro-and macro-morphological characters by using Stereomicroscope, light Microscope and Scanning Electron Microscope (SEM). These species include Fagonia arabica L., Fagonia bruguieri DC, Fagonia cretica L., Fagonia glutinosa Delile, Fagonia indica Burm., Fagonia microphylla Pomel, Fagonia sinaica Boiss, Fagonia schweinfurthii Hadidi, Fagonia tenuifolia Steud. and Fagonia thebaica Boiss. This study has elucidated the importance of the vegetative macro characters in the taxonomy of the genus as first step in identification, especially the length of the spiny stipules and the type of leaf blade. Leaf or leaflet shape as well as margins and apices are of minor taxonomic importance. Microcharacters can be used to recess the identification and can be consider as the second step in identification. An identification key has been constructed and the previous trials of classification have been discussed according to the obtained results.