Although most microbes are not readily cultured in the lab, microbial DNA can be extracted directly from an environmental sample and be functionally expressed in a suitable host for natural products discovery, and this approach has been termed "metagenomics". An E'mei Mountain soil metagenomic library was constructed using an Escherichia coli-Streptomyces shuttle vector for functional based screening of anti-bacterial clones in Streptomyces albus host. Two active clones were obtained and their fermentation broths were studied for the inhibitory effect on Staphylococcus aureus biofilm. Their fermentation products have a good inhibitory effect on the formation of S. aureus biofilm, and the inhibitory effect could exceed 90% when the concentration of sample was 2 MIC (Minimum Inhibitory Concentration). In addition, two samples had significantly effect on S. aureus biofilm dispersal, and the clearance rate of EM110 was higher than EM123. In conclusion, substances with strong bioactivities on biofilm formation and dispersal of S. aureus could be discovered by using metagenomics technology.