Leather tanning is a hard-hitting process where enormous amount of organic load was subscribed to treat the effluent; the treatment was carried out through the Common effluent treatment plant constituting physical, chemical and biological treatments. Apparently, the biomass which thrives in this extreme environment will own the ability to utilize the effluent i.e. the pollutants as the sole carbon source for its survival. Hence to explicit the nature of tannery effluent treatment setup and to employ the different modalities of molecular techniques for the identification of novel organism/gene for the treatment of the tannery effluent. The ultimate aim of the present chapter is to unmask the environmental genomes of tannery effluent at its different stages represents the different modalities on estimating the population richness and diversity with respect to their physicochemical parameters and treatment. The diversity of the population defined by conventional 16S rDNA sequencing majorly represents genera already reported in the public databases. However, diversity analysis using Next Generation Sequencing (NGS) tools reveals the presence of bacterial genus which is uncultivable in laboratory. Therefore, we conclude that it is essential to use both culture-dependent and culture independent methods to analyze the bacterial diversity as well as for their functional genes in any environmental niche.