The aim of this paper is to contribute to building a framework for reflexive governance of the information society. The hypothesis is that new institutional economics as an interdisciplinary research program can provide some of the necessary tools for this framework and help us to understand how the reflexive feedback of actors and users on the social challenges of the new technologies can be embedded in the institutions of regulation. To test this hypothesis, we develop a specific case study on the building of the microbiological commons. This case study is chosen because of the leading role of this field in the development of institutions procedures for reflexive involvement of actors and users in the institutional design, such as in the case of the Global Biodiversity Information Facility or GENBANK. As our analysis attempts to show, the success of these initiatives in building both efficient and legitimate means of information sharing is dependent on a double reflexive mechanism embedded in the institutional rules : (1) organizing feedback of the actors and users on the institutional rules and (2) the building of common understanding amongst different stakeholder communities.