Artemisia which produces a large number of secondary metabolites is naturally found in cold desert high altitude environment of India. Secondary metabolites such as alkaloids, flavonoids, phenols, polysaccharides and terpenes represent a significant barrier to the extraction of pure genomic DNA. Thus, in this study, the DNA extraction protocol to extract pure genomic DNA from different Artemisia species was tailored. The protocol was based on the CTAB method with slight modifications. In the study, 1.6 M NaCl, 2% cetyltrimethyl ammonium bromide (CTAB), 3% polyvinylpyrrolidone (PVP) and 0.5% β-mercaptoethanol was used in the extraction buffer. The incubation period was kept for 1 h at 65°C with one-tenth of the volume of warm (55°C) 10% CTAB solution during the extraction process. This study described a reliable protocol for extracting good quality and optimum amount of DNA from Artemisia species suitable for PCR analysis.Key words: Artemisia, genomic DNA isolation, PCR amplification, secondary metabolites.