In this study, a modified CTAB method combined with sodium sulphite and silica particles for the extraction of high-quality genomic DNA of recalcitrant plants such as malva, coffee, avocado, mango, olive, jatropha and tillandsia is reported. Maceration with liquid nitrogen, phenol treatment, RNase digestion and the ethanol precipitation step are eliminated using this methodology. The quality of the isolated DNA permits downstream molecular applications including AFLP, restriction, ligation and PCR amplification and sequencing of plant barcode genes (matK and rbcL). The cost per sample (about US$ 0.14) is quite low compared to any commercially available kit. This methodology is reproducible and could be used for a broad spectrum of woody plants with a high content of polyphenols and polysaccharides compounds, without the need for a commercial kit or expensive reagents, providing a viable alternative for laboratories with low budgets.