The conservation of biodiversity in highly fragmented landscapes often requires large-scale habitat restoration in addition to traditional biological conservation techniques. The selection of priority restoration sites to support long-term persistence of biodiversity within landscape-scale projects however remains a challenge for many restoration practitioners. Techniques developed under the paradigm of systematic conservation planning may provide a template for resolving these challenges. Systematic conservation planning requires the identification of conservation objectives, the establishment of quantitative targets for each objective, and the identification of areas which, if conserved, would contribute to meeting those targets. A metric developed by systematic conservation planners termed “irreplaceability” allows for analysis and prioritization of such conservation options, and allows for the display of analysis results in a way that can engage private landowners and other decision makers. The process of systematic conservation planning was modified to address landscape-level restoration prioritization in southern Ontario. A series of recent and locally relevant landscape ecology studies allowed the identification of restoration objectives and quantitative targets, and a simple algorithm was developed to identify and prioritize potential restoration projects. The application of an irreplaceability analysis to landscape-level restoration planning allowed the identification of varying needs throughout the planning region, resulting from underlying differences in topography and settlement patterns, and allowed the effective prioritization of potential restoration projects. Engagement with rural landowners and agricultural commodity groups, as well as the irreplaceability maps developed, ultimately resulted in a substantial increase in the number and total area of habitat restoration projects in the planning region.