Metagenomics is a revolutionary tool for genomic analysis of microorganisms. This involves the isolation and cloning of DNA from an assemblage of microorganisms. Metagenomics can also help identify potential biocontrol agents for fungi and bacteria that cause various plant diseases. Similar fungal species cause identical symptoms and are difficult to discriminate morphologically. Therefore, sequence-based identification is required. Therefore, multidisciplinary approaches, such as next-generation sequencing and sequence databases, are preferred to detect genotype- and species-level identification of pathogenic fungal plant pathogens without using traditional culture methods. Moreover, metagenomic data obtained from many studies are a promising and emerging method for identifying fungal diseases in plants. In this chapter, we focus on the role of metagenomics in the identification of biocontrol agents for plant disease diagnostics and their promising future developments.