A protocol is developed for the incorporation of multiple criteria, including spatial design and socio-political criteria, into the design of conservation area networks. This protocol begins with the identification of the non-dominated set of alternatives, where each alternative is a network of conservation areas that satisfies biodiversity representation targets. This set is then refined to identify a finally preferred alternative using a modification of the Analytic Hierarchy Process. This modification ensures that the results obtained are identical to those that would be obtained using standard multiattribute value theory while allowing the use of the transparent preference method of the Analytic Hierarchy Process. The final stage of the protocol consists of sensitivity analyses to test the robustness of the ranking of the alternative set. The protocol is applied to a practical data set from northern Namibia to identify a set of land units that can be targeted for biodiversity conservation beyond the existing national parks. Keywords: Analytic hierarchy process, Multi-criteria decision making, Multi-criteria analysis, Namibia, Trade-offs.