Metagenomics is the genomic analysis of microorganisms by direct extraction, cloning, and analyzing microbial genomics of DNA from their environments. Microorganisms constitute two thirds of the Earth's biological diversity. As many as 99% of the microorganisms cannot be cultured by standard techniques. Metagenomics approach have been developed to capture unexplored microbial diversity to overcome the existing barriers in estimating diversity, studying ecological interaction of organisms and comparative analysis for monitoring environment changes. Besides, it can also be applied to biotechnology. In this review, we outlined the process of metagenomics and its application and prospect in forestry, contributing to the development of forest science research.