In biodiversity-rich landscapes that are developing rapidly, it is generally impossible to delineate land use and prioritize conservation actions in relation to the full variability of species and their responses to anthropogenic activity. Consequently, conservation policy often focuses on protecting habitat used by a few flagship, indicator or umbrella species like tigers Panthera tigris and Asian elephants Elephas maximus, which potentially leaves out species that do not share these habitat preferences. We demonstrate an empirical approach that clustered 14 mammals into surrogate groups that reflect their unique conservation needs. We surveyed a 787 km2 multiple-use area in the Shencottah Gap of the Western Ghats, India, using foot surveys and camera-trap surveys. Using ecological niche factor analysis, we generated indices of species prevalence (marginality and tolerance) and habitat preferences (factor correlations to marginality axis). We then clustered species by both of the above index types to reveal four clusters based on prevalence and four clusters based on habitat preference. Most clusters contained at least one threatened species. Low-prevalence lion-tailed macaques Macaca silenus and tigers were strongly associated with closed forests and low human disturbance. But elephants, sloth bears Melursus ursinus and gaur Bos gaurus were more tolerant of anthropogenic impact, and sloth bears and gaur preferred open forests and grasslands. Dhole Cuon alpinus and sambar Rusa unicolor were associated with highly anthropogenic habitat (farmland, cash crop and forestry plantations) with high human use. Thus, reliance on flagship species for conservation planning can both underestimate and overestimate the ability of other species to persist in multiple-use landscapes; protecting flagship species would only protect species with similar habitat preferences. For species that avoid human impacts more than the flagship species, core habitat must be protected from human disturbance. For more tolerant species, conservation in anthropogenic habitat may hinge on policies that bolster coexistence with humans.