Artemisia annua is a medicinal plant that produce artemisinin, which has antimalarial activity. Artemisinin biosynthesis pathway depends on number of genes such as ADS, CPR and CYP71AV1. we studied gene structure of three genes which exhibit ADS gene possess 4 introns and 5 Exons with length 1794bp, CPR has to analyze the sequences of these genes, the CPR gene contains 6 introns and 7 exons with length 1633bp and CYP71AV1gene has 1 intron and 2 Exons with length 1554bp. Cis-acting elements detection in ADS, CPR and CYP71AV1 promoters revealed several such W-box , WRKY , TATA-BOX,CAAT-BOX ,IBOX MYC ,EBOX,GATA-BOX, which could be involved in gene expression regulation of artemisinin production genes. Our genes could be influenced by different external affects as light, cold, drought and elicitors which in turn may be due to an effect on the amount of artemisinin produced. ADS, CPR and CYP71AV1 proteins evolution shows Artemisia annua, and Tanacetum cinerariifolium always are closed in one cluster which refers to a common ancestor of those two genotypes.