Isolation of DNA sufficient in purity, large in fragment and high in diversity from natural environments is the basis for molecular ecology study on community structure. In this study, the authors chose an indirect method, which is the cell recovery method, to extract DNA from two distinct red soils in South China, calculate its recovery efficiency and compare with the direct method in DNA yield and purity. The results show that the crude DNA yields from the two soils were about 0.34 and 0.53μg/g by the indirect method and 13.62μg, and 24.32μg/g dried soil by the direct method respectively. Although the indirect DNA extraction method recovered smaller amounts of total DNA than the direct method, the DNA fragments are larger in size. Moreover, the results of Sau3AⅠ enzyme digestion and PCR amplification in evaluating DNA purity demonstrate that the indirect method can delete some inhibitor more efficiently, yielding DNA of superior quality more suitable for follow-up procedures.