In this paper, we present the Inter-Institutional Gap (IIG) framework as a novel approach to conceptualizing the often-overlooked interconnectivity of different rule-levels between formal and informal institutions in a natural resource system. This framework goes beyond the existing concepts of legal pluralism, institutional void, structural hole, and cultural mismatch, each of which offer valuable insights to particular gaps between formal and informal institutions, but do not sufficiently address the interaction at every rule level (i.e. constitutional choice, collective choice and operational choice rules). In order to demonstrate the potential of our framework for better understanding the underlying causes of inter-institutional gaps, we apply it to four case studies that encompass diverse geographical locations, governance levels, and social-ecological systems. Results reveal that institutional gaps tend to exist when there are unintended, unforeseen or hidden gaps between the different rule levels operating among the different institutions involved in governing a single resource system. More specifically we observe that: (i) inter-institutional gaps are co-existing, therefore if a certain gap is identified, other gaps may be expected; (ii) certain gaps may reveal latent gaps; and (iii) intermediaries may be key to addressing inter-institutional gaps. In many cases, sustainable natural resource management and regulation cannot be achieved without directly addressing the inter-institutional gaps that exist between formal and informal institutions operating in the same resource system. The framework facilitates analysis and understanding of multi-level governance structures in pursuit of addressing complex natural resource management issues.