Amorpha-4, 11-Diene Synthase (ADS) gene is the first and important gene in artemisinin biosynthesis pathway that why for many researchers, the study of how to regulate of this gene is important. Transcription factors can change the expression rate of several genes simultaneously. In this study, six wild accessions of Artemisia annua, collected from Golestan province, were used. Many known transcription factors were identified by three cis-element databases PLATcare, TRANSFAC and PLACE in ADS promoter, such as many light-responsive elements, cis-acting regulatory element involved in the biotic and a biotic stress and Regulate MYB TFs involved in secondary metabolites. Phylogenetic tree of two new putative transcription factor of Artemisia annua showed a high similarity with other MYB family of transcription factors. In order to compare the genetic effects of different transcription factor, we used natural genetic potential, it means, different ecotypes with different genetic potential. In comparison of two plants 6 and 3, the results showed that the expression rate of three transcription factors were high, but the expression rate of ADS gene was low, it means, we cannot change the expression rate of ADS gene by over expressing of these transcription factor in plant 3. According to these result we can conclude that the promoter of ADS gene does not have necessary cis-element to load the transcription factors. In this reason, they could not change the expression rate of this gene however they are over expressed. Ecotype 3 and 4 had the lowest and highest expression rate of four genes, respectively. The result of comparison of different genes in different ecotypes showed that WRKY and puMYB1 transcription factors have more important role than puMYB2 transcription factor.