Dr. YS Parmar University of Horticulture and Forestry, Nauni-Solan, IndiaMicrobes are ubiquitous in nature, and exist as the true elixir of mankind. The estimated number of microbial cells on Earth hovers around to be 10 ³⁰. The conventional microbial techniques enable us to grow microbes in the laboratory and study them under in vitro conditions. But those techniques are not powerful enough to culture diverse microbes at once, as they are time-consuming and contamination prone. Omics sciences have become core scientific tools to characterize microbiomes and study the natural communities and discover new microbes and their genes from the environment at a real fast time. Metagenomics seems to be the ideal culture-independent technique for unravelling the biodiversity of samples in addition to its clinical and diagnostic approaches. Metagenomics is the study of genomes recovered from the environmental sample using the advanced bioinformatics tools and genetic technologies This Omics approach is a vast field of growing interest among the scientific community and the need for efficient cultivation strategies has led to many rapid methodological and technological advances. The most difficult issue for the user is definitively not to get lost among all possible choices. Genome-resolved metagenomics, an amazing hypothesis generator, has revolutionized our ability to understand the uncultured microbes and catalysed unprecedented discoveries that have impacted the multiple fields from biogeochemistry to evolutionary biology. Thus, in this review, we have quantified the development of metagenomic application in examining the microbial ecology and we have also discussed some of the important informatics tools deployed in the metagenomic studies.