In the past two decades, metagenomics has developed as a quintessential technique and has revolutionized various sectors of biological sciences and biotechnology. Metagenomics is a new technological aid which holds answers for lot of queries related to uncultivable microbial population. Metagenomics is done for the wild organisms to study about their genome and to seek pivotal insights from it. There is a huge diversity of microbes which cannot be studies in laboratory, but is of high significance in more than possible ways, one can even think of. Henceforth, metagenomics is conducted utilizing chronological techniques which can be manifested to draw considerable understanding about the unknown population. So far, various domains have been explored by the use of metagenomics and are described ahead in this chapter. Metagenomics can be seen in amalgamation with a lot of conventional practices to bridge the gap in research. There are several challenges which are to be answered yet, when the broad canvas of metagenomics is analysed and thus, there is a need to debate on such challenges.