DNA isolation from plants is sometimes difficult due to the existence of high levels of endogenous phenolics, polysaccharides, or other substances that may interfere with DNA extraction. Theobroma cacao produces high levels of anthocyanins in young leaves. These plant polyphenols can interfere with DNA isolation. After examination of various procedures for DNA isolation, two commercial isolation procedures have proved to be repeatedly successful using these types of plants, the D(2) BioTechnologies DNA X-tract Plus kit and the Qiagen DNeasy Plant System DNA kit. These commercial kits were chosen for their speed and ease over the CTAB procedure, which is more labor intensive. All protocols assessed yielded DNA suitable for AFLP or SSR procedures. An additional factor in DNA extraction efficiency is the degree of cell breakage, which may be more difficult with the highly fibrous leaf tissue that is found in many monocots, including date palm. Two commercially produced pieces of equipment were tested and, for cacao, both resulted in template DNA yielding amplification product in AFLP or SSR fingerprinting. However, for the fibrous date palm leaf, the larger FastPrep homogenizer consistently yielded DNA that generated higher signals when amplified than did the smaller Disruptor Genie.