This article explores the impact of the Nagoya Protocol to the Convention on Biological Diversity on the complex of international institutions involved in the governance of access to, and benefit sharing from, genetic resources. Conceptually, we develop an interplay management perspective that focuses on the governance of institutional complexes and their internal division of labor by means of collective decisions within the elemental institutions. We seek to understand interplay management with reference to constellations of actors’ interests and power, as well as institutional factors (commitments, inter-institutional consistency). We argue that the strength of status-quo forces led to the Nagoya Protocol consolidating and clarifying (rather than changing) the existing inter-institutional division of labor. The analysis demonstrates the difficulty of changing existing inter-institutional balances, yet suggests that a consolidation of an inter-institutional equilibrium can induce important new, path-dependent developments in fragmented governance architectures.