Transnational exchanges of plant, microbial and animal genetic resources are essential for scientific and agricultural research as well as for downstream commercial applications in fields such as food security and medicines. Under the Convention on Biological Diversity (CBD), the use of traditional knowledge associated with genetic resources requires the permission of relevant Indigenous populations, while the Nagoya Protocol to the CBD requires all member countries to cooperate in cross-border enforcement of the CBD’s provisions. This paper recommends that the Microbial Research Commons adopt a science-friendly governance structure that improves upon the scheme implemented by the Food and Agriculture Organization’s International Treaty on Plant Genetic Resources for Food and Agriculture, and incorporates the World Data Centre for Microorganisms.