Six DNA extraction methods and four DNA purification methods were compared and analyzed in this study to get higher quality DNA from the rhizospheric soil of Fritillaria thunbergii Miq. Results showed that higher purity DNA were harvested by pretreating the soil with 20 mmol/L EDTA (pH 7.5), then isolating soil DNA with CTAB-SDS-frozen-thawing, and further purified by agarose method. The recovery rate of this soil DNA was about 44.00 μg/g ± 2.65 μg/g soil, and they were qualified for the microbial diversity analysis in the rhizospheric soil of F. thunbergii Miq based on the 16S rDNA sequence.