For the last several years, Actinobacteria have been represented as the major storehouse for the production of natural products. Recent studies have shown that the plant rhizosphere soil comprises several plant growth-promoting Actinobacteria. Analyzing the actinobacterial genes in the rhizosphere of plants, especially those associated with plant growth promotion, plays an important role in improving soil fertility and crop productivity. As in high-throughput genome sequencing methods, there is a drastic development in the discovery of novel compounds produced by Actinobacteria. As many Actinobacteria are culturable in the lab, non-culturable Actinobacteria from rare or unexplored ecosystems are found to be in special attention, especially from the sequencing of DNA from within the constituent community. The construction and screening of metagenomic expression libraries have great potential to identify novel genes and their functions. In this chapter, we describe briefly metagenomic library preparation from rhizosphere actinobacterial DNA, screening of libraries for growth-promoting genes, and a computational pipeline for high-throughput assembly and annotation of functionally selected DNA.