The purity of DNA is one of the major factors affecting the success of Genomic studies. Nucleic acid isolation from polyphenol rich plants fail to produce good quality DNA or RNA as polyphenols adhere and interfere with DNA during isolation. An improvised, simple and inexpensive protocol has been developed for extracting genomic DNA from Mulberry (Morus spp.). The purity of the DNA as revealed by the ratios of absorbance at 260/280 nm (A 260/280) and 260/230 nm (A 260/230) was closer to 2.0. Genomic DNA analyzed for analytical applications like restriction digestion and PCR amplification with molecular markers viz., Inter Simple Sequence Repeats (ISSR), Random Amplified Polymorphic DNA (RAPD) and Simple Sequence Repeat (SSR) primers further confirmed the purity of the DNA. A modified method of silver staining was employed for the resolution of SSR amplified products. Physiologically mature leaf was found more suitable for getting quality DNA in mulberry.