Results are reported of an analysis of the conflicts that the zoning of marine protected areas might generate in the Galapagos and San Andres archipelagos given the involved stakeholders' competing interests. This will assist stakeholders, including the final decision makers, to develop cooperation strategies for managing conflicts. Specifically, the analysis focused on the stakeholders' conflicting priorities for a number of criteria deemed relevant to the evaluation of alternative geographical zoning configurations. Sets of statistically similar priorities are suggested as bargaining positions to those stakeholders who find it advantageous to seek cooperation with others sharing the same values instead of acting alone when debating MPA zoning alternatives. Another result that will contribute to cooperation strategies is the assessment of the solidarity of cohort groups of stakeholders as reflected by the extent of similarity among their priorities. © 2006 Elsevier Ltd. All rights reserved.