Functional overlap in the jurisdiction and competencies of international agreements can lead to incomplete and contradicting regulation, which erodes benefits form international cooperation. The framework developed in this paper seeks to further the theoretical analysis of the domestic and international determinants for the origin and the persistence of such incoherence. Using international regulation on the conservation of plant genetic resources as an illustrative example I address two theoretical challenges - the problem of cross-level inference in theories of international cooperation and the differentiation of processes of substantial bargaining from those of negotiated institutional change. Substantial bargains can be formally analyzed as two-level or nested games with variable payoffs, whereas rigorous analysis of institutional change is limited by too many variations in game structure. I use the framework to derive a typology of games for guiding the systematic analysis of the international, domestic and cross-level interactions that may offer explanations for the phenomenon of incoherence due to functional overlap.