Abstract: A comparative study was conducted on the results of DNA concentration, removal rate of humic acids, PCR amplification of 16S rDNA, restriction endonucleases of amplified fragment and the denaturing gradient gel electrophoresis of the microorganisms isolated from 3 types culture substrates with 4 DNA extraction protocols.The results showed that the humic acids could be effectively removed by precleaning the samples with CaCO3 buffer, cell lysis process synergically assisted with CTAB buffer and proteinase K and adding 2% CaCl2 into the reaction solution. The DNA quality was improved after being precipitated by PEG 8000 and then purified by Sephadex G-200 spin column. The DNA obtained by this way was qualified for PCR amplification and restriction endonucleases analysis with ARDRA technique. This kind of DNA extraction might be applied to DGGE analyses and to express the diversity of microbial populations.