The breakthroughs in microbiology have allowed us to come to terms with the microbial resources present in culture collections and in natural environments. The challenge at present is to manage these microbial resources, particularly when one deals with open systems where the dynamics of microbial ecology are predominant. Hence, to properly address the aspects of Microbial Resource Management (MRM), one needs to handle the questions of who is there, who is doing what with whom and how can one adjust, control and/or steer these mixed cultures and communities. It is argued that microbial ecologists and environmental microbiologists need to address a new mind‐set. The Beijerinck axioma that all microorganisms are everywhere should not be presumed to be generally valid. The Darwin based niche assembly concept needs to be supplemented with the neutral theory of Hubbell. The Pareto 80/20 principle is also applicable to the macro‐economies of microbial communities. Finally, the concept of a “stable” microbial community should be replaced by that of a cooperative community continuum. Overall, MRM is at the basis of a number of new developments in domains such as environmental safety and health, renewable energy production, closing environmental cycles and providing new materials. Specific examples such as, for example, pro‐active immuno‐stimulation by means of drinking water, electro‐microbiology, decreasing global warming by implementation of methanotrophs and generation of nano‐biocatalysts are discussed.