Population genetic and phylogenetic analyses of plant species are often limited by time-consuming DNA extraction and purification procedures. We developed a rapid protocol for the isolation of genomic DNA from gymnosperms using silica-based membranes in a 96-well plate format. This protocol yields high-quality DNA as evidenced by PCR-amplification of chloroplast DNA and RAPD-PCR analyses. The DNA quality was higher than that observed for DNAs isolated using a one-tube extraction process.