In environmental microbiology, molecular ecology study has been widely concerned in the world, while high quality DNA is the basis of the study. In our study, soil microbial DNA was extracted by the methods of SDS lysis denaturant plus SDS lysis, and purified with gel electrophoresis plus minicolumn and double minicolumn methods. The results showed that denaturant plus SDS lysis could extract DNA more efficiently, and gel electrophoresis plus minicolumn could help to obtain purer DNA that was available in amplifying its 16S rDNA and functional genes by PCR. Therefore, denaturant plus SDS lysis could be an efficient and reliable method to extract DNA molecular ecology studies.