This dataset presents the results of an analysis to characterize the distribution of conservation values across the Mojave Desert Ecoregion. Using an ecoregional planning approach followed worldwide by The Nature Conservancy and its partners, we identified a suite of conservation targets (521 species, 44 ecological systems, and seeps and springs are the focus of the plan) and set quantitative conservation goals for each target. We also characterized land-use impacts across the desert, such as roads, urban areas, and agricultural uses. We then used Marxan conservation planning software to help identify and map the relative conservation value of lands across the region for meeting the stated conservation goals. Our analysis involved dividing the entire Mojave Desert Ecoregion into one-square-mile (259-hectare) planning units, synthesizing spatially-explicit information on the conservation targets and anthropogenic disturbance found in each planning unit, and then using this information to identify the relative value of each planning unit in meeting our conservation goals. High conservation value was attributed to areas with low levels of disturbance and unique conservation target occurrences or high concentrations of target occurrences.