Abstract: This study analyses the effectiveness of 12 previously published DNA extraction protocols (used for the extraction of DNA in various species) in contrast to 3 commercially available plant DNA extraction kits. In addition, an innovative, sonication-based, simple and efficient mini-prep to extract DNA from chrysanthemum, tobacco and Spathiphyllum were presented. DNA purity and quantification, EcoRI-restricted total genomic DNA and RAPD analyses using three separate 10-mer primers and 5 primer sets (5SP3/4, NT107-1/2, LFY3, trnh and trnK2R) show differences in the efficiency and applicability of the extraction method, even within the same clonal cultivar. Variation between explant source may be related to cytological endopolyploidy, 8C cells abundant in callus, with between 1-5% 16C cells. These factors should be carefully considered when selecting a DNA extraction protocol or source of plant material for somaconal variation or population genetic studies, or for transgene integration analyses.