DNA analysis is an effective method for wood identification. Obtaining sufficient quantity and quality DNA is the prerequisite. In this paper, Dalbergia odorifera T. Chen of Leguminosae sp. family was selected as material. Three methods, i.e., modified CTAB, DNeasy Plant Mini kit (QIAGEN) and PTB (N-phenacylthiazolium bromide) were employed to extract the DNA in sapwood and heartwood. The quality and quantity of the DNA extractions in the two zones were compared to explore the proper methods for extracting DNA in different parts of wood. The results showed that the concentration of DNA in sapwood and in heartwood isolated by the three methods ranged from 75.95-937.38 ng·μL^-1, 4.46-806.56 ng·μL^-1, respectively. The maximum value of DNA concentration was reached by the PTB method in sapwood and heartwood, meanwhile, the minimum value was reached by the kit method. The target sequence of DNA in sapwood isolated by the three methods was amplified successfully after being purified, while the DNA in heartwood isolated by the PTB method were subjected to polymerase chain reaction after being purified. The DNA in sapwood can be extracted by the three methods, but the DNA in heartwood can be extracted more suitably by the PTB method.