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In this paper a methodology for evaluating the feasibility of economic subsidies on land use systems using local indicators of sustainability in the Constitucion region, Calakmul, Campeche (Mexico), is proposed. In order to identify the sustainability indicators for evaluating the Jalapeño pepper (Capsicum annum L.), and Maize (Zea mayz L.) crop systems, local farmers, policymakers and agronomists were interviewed and a list of 17 indicators were obtained. Both evaluating models were approved by the Municipal Council for Sustainable Rural Development of Calakmul (CMDRS), committee that endorses subsidies to farmers through an application contest. The Jalapeño pepper got 69.40% and the Maize crop system got 54.10%. The main identified limitations in both crop systems are the lack of crop-production technologies, lack of organisation among farmers and deficient trading of the harvests. The methodology proposed here, is meant to help farmers, policymakers and agronomist to identify the main limitations in the production of the regional main crop systems, in order to invest the scarce resources in solving this problem. We believe the methodology could be applied in other regions of Mexico; so far the indicators are adjusted to local conditions of each region to be used. [ABSTRACT FROM AUTHOR]