Endophytic actinomycetes, Gram-positive filamentous bacteria, live inside the plant tissues of different organs including roots, stems, leaves, flowers, fruits, and seeds. They not only harm the living plants, but also have proper effects on their host plants such as promoting plant growth and defending phytopathogens. Numerous classes of bioactive natural compounds, polyketides, macrolides, alkaloids, peptides, and terpenes, with various bioactivities: antibacterial, antifungal, anti-phytopathogens, immunosuppressant, anticancer, antioxidant, and anti-inflammatory, were produced by Streptomyces kebangsaanensis, Streptomyces albidoflavus, Actinoallomurus fulvus, Micromonospora lupini, M. endophytica, Polymorphospora rubra, and Streptosporangium oxazolinicum strains. Moreover, their novel compounds are also continued to discover and develop for preclinical stages. Thus, endophytic actinomycetes are the most key sources of potential bioactive metabolites, as well as a reservoir to mine for novel chemical structures. Moreover, with the progress in high-throughput genome sequencing techniques, many genome mining methods has been developed and helped to link the discovered compounds to their biosynthetic gene clusters (BGCs). This chapter highlights bioactive compounds derived from endophytic actinomycetes on their biological activity and biotechnological potential together with the modern disciplines, and genome mining tools for discovery of the novel compounds. © The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd. 2022.