Artemisia is a large, diverse genus of aromatic plants with various medical and nutritional, as well as landscape usage. Artemisia species are a source of various anti-malarial, cytotoxicity, antibacterial and antifungal effects, and antioxidant properties which are due to sesquiterpene compounds. In recent decades, A. annua has been attracted a great deal of attentions because of its artemisinin which is a sesquiterpene lactone and has anti-malarial effects. The amount of artemisinin production varied in different species. Recently, artemisinin is used against a malaria pathogen, Plasmodium flasiparum , which has a multidrug resistance. Unfortunately, production of artemisinin in plants is very low and its chemical synthesis is very difficult and expensive. In recent years, many efforts have been done to increase the expression of genes and enzymes which are involved in artemisinin biosynthesis. In order to evaluate the effects of changed in expression of artemisinin producing genes, the real time polymerase chain reaction is used. This technique is sensitive enough to measure the low mRNA copy number. The errors of RNA degradation possibility, difference of RNA concentrations in different samples and also technical errors may be accrued during the real time PCR. For control of these errors, selecting an accurate method for normalization is important. Among abundant methods of normalization, using housekeeping genes as internal controls in the analysis of gene expression is in general. The expression levels of these genes should be stable in tested tissues or cells and significant changes should not be occurred under experimental conditions. However, the expression levels of these reference genes in different tissues and organs are different and for each genotype and tissue, one or several suitable internal control genes should be selected carefully. In this study, the stability expression of seven genes includes act , pal , cpr , 18S rRNA , EFl ?, UBQ and RPS9 were studied in different tissues of Artemisia species ( A. annua, A. absinthium, A. sieberi , A. dracunculus and Artemisia sp .). RNA was extracted from leaf, stem and root tissues, and cDNAs were synthesized. All data obtained from real time PCR were analyzed by Finder Norm software to estimated suitable genes. The results showed that among the various tissues of the Artemisia species, RPS9 gene is the most reliable internal control gene. Combination of UBQ and 18S rRNA genes was recognized the best combination for gene normalization among Artemisia species. These results show that housekeeping genes are regulated completely different in various kinds of plant species and they have different expression patterns. Since a reference gene with a stable expression in an organism may not be suitable for normalization of gene expression in other organisms or different experimental conditions, it is essential to varify its validity before application. The analysis of these genes in different tissues also confirmed the stability of RPS9 gene and the combination of RPS9 and 18S rRNA genes can be applied in different tissues of Artemisia genus. The amount of artemisinin measured in several species of Artemisia available in Iran, was performed with a hollow fiber micro extraction method. The results showed that the level of artemisinin in leaves were much higher than stems and also the amount of this valuable material in A. annua is more than other species. Key word : Artemisia, Artemisinin, Reference gene, Normalization, Real time PCR.