A new method was developed to screen for antibiotic microorganism producing strains from soil using metagenomics. Six different environmental soils metagenomics DNA were extracted with liquid nitrogen freezing method and purified by polyvinylpolypyrrolidone (PVPP) column chromatography. Soil DNA of 32.25?61.25 μg with DNA length about 23.1 kb can be extracted from 1 g sample. 16S rDNA can be amplified from the purified soil DNA which proved that the extracted soil DNA is suitable for following experiments. In addition, the sensitivity and feasibility of this screening method is evaluated by addition of Herbimycin producing strain into a negative soil. The result showed that when the soil contains 103 CFU/g of Herbimycin producing strain, the Herbimycin biosynthesis gene can be detected by PCR and the incorporated known strains can also be isolated. These results suggest that soil metagenomics can be applied for screening certain antibiotic microorganism producing strains which is sensitive and rapid, and is more efficient than the traditional methods.