Actinomycetes, Gram positive soil bacteria, are valuable microorganisms which produce useful secondary metabolites including antibiotics, antiparasitic substances, anti-cancer drugs, and immunosuppressants. Although a major family of actinomycetes, known as streptomycetes, has been intensively investigated at the molecular level for several decades, a potentially valuable and only recently isolated non-streptomycetes rare actinomycetes (NSRA) family has been poorly characterized due to lack of proper genetic manipulation systems. Here we report that a PCR-based genome screening strategy was performed with approximately 180 independently isolated actinomycetes strains to isolate potentially valuable NSRA strains. Thanks to this simple PCR-based genome screening strategy we were able to identify only seven NSRA strains, followed by 16S rRNA sequencing for confirmation. Through further bioassays, one potentially valuable NSRA strain (tentatively named Nocardiopsis species MMBL010) was identified which possessed both antifungal and antibacterial activities, along with the presence of polyketide synthase and non-ribosomal peptide synthase genes. Moreover, Nocardiopsis species MMBL010, which was intrinsically recalcitrant to genetic manipulation, was successfully transformed via E. coli-driven conjugation. These results suggest that PCR-based genome screening, followed by the establishment of an E. coli-driven conjugation system, is an efficient strategy to maximize potentially valuable compounds and their biosynthetic genes from NSRA strains isolated from various environments.