Abstract: Microorganisms produce secondary metabolites with diverse structures and significant activity, which provides abundant natural compounds for drug discovery. However, it is difficult to meet the requirement for rapid discovery of novel microbial drugs by traditional research models, and new strategies are urgently needed. With the advent of the genomic era, researchers have developed a series of genome mining strategies and explored various genome-directed new natural product discovery patterns, among which the natural product discovery strategy based on self-resistant genes shows broad prospects. In the struggle for survival in nature, self-resistance is the key to ensuring that toxic natural products producing microorganisms "kill enemies without harming themselves". Studies have found that self-resistant genes can also provide effective clues for genome mining and discovery of natural product activities. Here, the review aims to summarize the main self-resistance mechanisms in microorganisms, genome mining strategies based on self-resistant genes and their application in natural product discovery, and briefly describe the relevant bioinformatic tools, so as to provide new insight for discovery of bioactive natural products.