Environmental microorganisms form an invaluable natural reservoir of new enzymes and bioactive compounds. Research in the last two decades, particularly the application of environmental genomics (metagenomics) and microbial genomics, has started to demonstrate the potential of environmental microorganisms in bioindustry. Here, from an environmental microbiologist point of view, I will discuss two technical considerations in the application of environmental microbiology in biotechnology, 1) success and frustration of current metagenomic approach and how to improve it; 2) the error and impreciseness of gene annotation in public database, why should biotechnologists care about it and how can we address it.