Incentive-based management is an encouraging option in the quest for sustainability, and the Marine Stewardship Council (MSC) is the most prestigious certification standard. It implies sustainability and resilience, but the latter has yet to be explored. Accordingly, we selected two MSC-certified fisheries, the small-scale red lobster fishery (RL) in Baja California (BC) and the small pelagic industrial fishery in Sonora (SP), to prove whether the certification success is reflected in a resilient governance network structure. To do so, we identify structural patterns that drive the resilience of the governance network in two MSC-certified fisheries. Data obtained through stakeholder interviews on different types of stakeholder relationships were used to construct weighted communication matrices to model governance networks. We assessed the individual role of each actor using centrality indices. We also analyzed how stakeholders are integrated into cohesive subgroups of the network. To evaluate resilience, we compared changes in the structure of governance networks by analyzing how network properties change each time the loss of an actor and/or its functionality is simulated. In both fisheries, most of the stakeholders belonged to the productive sector, actors involved in capture, processing, commercialization, and industrialization in the case of SP. For all centrality indices, the most relevant actors were similar or the same in both fisheries and belonged mainly to the regulatory and productive sectors. Cohesive subgroup analysis revealed that both networks are highly connected and collaborative systems. The simulations showed that in both fisheries, the decrease in the number of stakeholders did not cause abrupt changes in the structure of the governance systems. This approach reveals that, even in worst-case scenarios, the tolerance of governance systems to this severe loss of stakeholder diversity is high and suggests that following sustainable certification standards can lead to the promotion of effective and resilient governance networks.