Traditional bioassay-guided natural product discovery has led to re-isolation of a large quantity of known compounds, and thus dramatically stunted the process of drug development. Large-scale genome sequencing revealed the existence of numerous cryptic biosynthetic gene clusters in microbes, which have attracted increasing attention in the research field of natural product discovery. In this review, we summarized the strategies for activation of microbial cryptic gene clusters at pathway-specific and pleiotropic levels, and discussed trends in structural identification technologies used for genome-guided compound mining. Activation of cryptic gene clusters will open new era for effective discovery of novel bioactive natural products.