The intricate problems pertaining to the modification of human and environmental microbiota are critically examined in this chapter. The conflict between human rights and scientific advancement is exemplified by ethical concerns such as informed consent, data privacy, genetic editing and equitable access. The ongoing ambiguity and fragmentation of the regulatory environment including differing definitions of microbiota-based therapies such as foods, medications or biologics complicates approval procedures and market authorization. Numerous ethical and regulatory issues have arisen as a result of the quick development of microbiota research and its growing applications in biotechnology, healthcare and agriculture. These issues need to be carefully and quickly considered. This section’s thorough analysis of these urgent issues lays the groundwork for future discussions and the development of legislation intended to promote moral innovation in microbiota research. Commercialization attempts are complicated by a number of issues including intellectual property rights, bio-prospecting, benefit sharing, public misconceptions, cultural sensitivities and the environmental impact of releasing engineered microbial strains.