Abstract (141 words) Several extraction methods of genomic DNA with the purpose of species identification and characterization of genetic diversity in numerous fern species are being used currently. However, it is important to identify which extraction method is the best in removing the presence of undesirable compounds in fern sample mainly polysaccharides and polyphenols. High contents of polysaccharides and polyphenols increase the sample viscosity and decrease the DNA quality, which will interfere with PCR performance. Therefore, this study evaluated the quality of genomic DNA extracted using commercial plant extraction kit and modified CTAB extraction method to compare consistency of both methods for several common fern species in Peninsular Malaysia. Results showed the efficiency of the modified CTAB extraction method compared to kit extraction method. The genomic DNA isolated was found to be relatively pure and suitable for phylogenetic as well as conservation genetic studies.