[Background] Rare actinomycetes represent a “new treasure trove” for discovering natural products. Studies remain to be carried out to explore the natural product-producing potential of Saccharothrix as typical rare actinomycetes. Furthermore, few studies reported gene editing systems specifically tailored for Saccharothrix. [Objective] This study aims to elucidate the potential of Saccharothrix in synthesizing natural products with diverse structures. Additionally, we seek to establish gene editing systems for representative strains, thereby fostering the discovery of novel natural compounds and advancing the research on related biosynthetic pathways. [Methods] Multi-locus sequence analysis (MLSA) was employed to assess the similarity among 34 publicly available Saccharothrix genomes. The tool antiSMASH was utilized to analyze the gene clusters and the structural information of associated products. Additionally, BiG-SCAPE was applied for clustering analysis of these gene clusters. The representative strains, Saccharothrix australiensis DSM 43800 and S. syringae NRRL B-16468, were selected, for which the conjugation transfer and gene editing systems were established via integrative vectors and gene knockout vectors. [Results] The analysis of the 34 Saccharothrix genomes revealed a total of 1 348 natural product biosynthetic gene clusters , with an average of approximately 40 clusters per genome. The gene clusters were abundant in the biosynthesis of polyketides, non-ribosomal peptides, hybrid products of polyketides and non-ribosomal peptides, as well as ribosomally synthesized and post-translational modified peptides. The 1 348 gene clusters were grouped into 852 gene cluster families (GCFs), which were further grouped into 130 gene cluster clans (GCCs). This study established and optimized a conjugation transfer system applicable to S. australiensis DSM 43800 and S. syringae NRRL B-16468. Additionally, gene editing systems were successfully established for the two representative strains, with the establishment of corresponding mutant strains. [Conclusion] As rare actinomycetes, Saccharothrix exhibit a rich array of natural product biosynthetic gene clusters , highlighting robust potential for synthesizing diverse natural compounds, particularly polyketides and polypeptides. Moreover, this study achieves precise editing of the Saccharothrix genome, laying a solid foundation for probing into the gene clusters and associated products.