Protected areas in India have historically been established on an ad hoc basis with little attention to the conservation value of an area. This study focusses on a set of protected areas in the Agastyamalai region of the Western Ghats (WG), India. We examine forest loss and land-use changes in the study area from the early 1900s to 1960 and from 1960 to 1990. We use GIS to perform a biodiversity gap analysis of the protected areas in the study site. We produce a detailed map of existing floristic types and use it to generate layers corresponding to floristic species richness, zones of floristic endemism, floristically unique areas, and habitat distribution of representative endemic faunal species. These layers are combined with a map of the protected area network to highlight areas of high conservation value excluded from adequate protection. Deforestation rates are high in the study region and several areas of high biodiversity value are excluded from the highest levels of protection. We offer this method as a step toward developing a utilitarian conservation value index for assigning conservation and management priorities.