The foundations of pharmaceutical biotechnology mainly lie in the capability of plants, microorganism and animals to produce low and high molecular weight compounds useful as therapeutics. Although molecules from plants and microorganisms are preferred extraction from plant biomass needs tedious downstream processing while in case of microorganisms it is easy with fewer amounts of impurities. Pharmaceutical biotechnology is poised to flourish for the last 4-6 decades with the advent of recombinant DNA technology and metabolic engineering supported by the well-developed bioprocess technology. Large scale production and cost effectiveness and affordability could be achieved by way of synergising all these technologies. In the current review importance of microorganism in conjunction with recombinant DNA technology is discussed for the production of biopharmaceuticals and development of therapeutic applications using recently developed molecular methods and mechanisms of disease progression. Bacterial enzymes are being used in applications from drug modification to therapeutic uses.