Ten Fagonia species grown in the Libyan Desert were subjected in this study. 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. Anatomical characters, include internal structures of both stem and leaves have been subjected in this study. Taxonomical key has been constructed according to internal structure of the stem. The result of the ANOVA tests indicate that five characters; stem outline, number of phloem fiber patches in the cortex, number of parenchyma layers in the cortex, ratio between xylem and vascular bundle; ratio between phloem and stem and ratio between xylem and stem; are highly significant different within the studied species. The previous trials of classification have been discussed according to the obtained results.
Key words: Desert plant- Fagonia- Leaf anatomy- Libya- Stem anatomy- Taxonomy.