The large diversity present in ecosystem has tremendous potential in the microbial bioprospecting. Microbial bioprospecting is a branch of science, which deals with the identification of suitable microorganisms, biological compounds, or gene sequences which can be used for useful compounds for human welfare. Computational approach to biology is one of the rapidly emerging and promising branches of science. In the past few years, there is dumping of enormous amount of biological data especially from microbial genomes and transcriptomes to public databases. To use these data for the improvement of quality and quantity of microbial products for sustainable development, one needs to expertize in computational methods. In this chapter we have discussed the computational tools (techniques and databases) for better understanding of microbial genes, genomes, and proteome. We have also discussed the importance and uses of next-generation sequencing (NGS) tools to understand microbial genetics and genomes for better production of microbial products such as antibiotics, fermented products, biofuels, etc. Application of these approaches, tools, techniques, and databases to understand the microbial genes, genomes, and proteome would have tremendous effect on development, improvement, and sustainable cultivation of microbes.