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Abstract: Marxan is the most widely used conservation planning software in the world and is designed for solving complex conservation planning problems in landscapes and seascapes. In this paper we describe a substantial extension of Marxan called Marxan with Zones, a decision support tool that provides land-use zoning options in geographical regions for biodiversity conservation. We describe new functions designed to enhance the original Marxan software and expand on its utility as a decision support tool. The major new element in the decision problem is allowing any parcel of land or sea to be allocated to a specific zone, not just reserved or unreserved. Each zone then has the option of its own actions, objectives and constraints, with the flexibility to define the contribution of each zone to achieve targets for pre-specified features (e.g. species or habitats). The objective is to minimize the total cost of implementing the zoning plan while ensuring a variety of conservation and land-use objectives are achieved. We outline the capabilities, limitations and additional data requirements of this new software and perform a comparison with the original version of Marxan. We feature a number of case studies to demonstrate the functionality of the software and highlight its flexibility to address a range of complex spatial planning problems. These studies demonstrate the design of multiple-use marine parks in both Western Australia and California, and the zoning of forest use in East Kalimantan. [Copyright &y& Elsevier]