Ecological indicators were synthesized to identify ecologically significant and priority areas within each province/administrative territory of Pakistan. We compiled the spatial distribution of six aspects of ecological value for geographical targeting of conservation priority areas. A Geographic Information System (GIS) based overlay analysis of ecological dynamics was carried out. Indices for forest cover, vegetation zones, endemic mammals, highly significant wetlands, bird species richness and mammal species richness were developed by compiling the secondary data into Geographic Information System. Analytical hierarchy process was used to weight these indicators and also multi-attribute utility theory to combine them into a single spatial layer of ecological value. On the basis of these indices each district was ranked within its respective province/administrative territory. The results highlighted ranking of districts in order of their ecological significance within the province for all the provinces/administrative territories. The study is a pioneer study to identify administrative areas of high ecological value and can guide in setting the conservation priorities. The current broad scale study can help decision makers in provincial level policy making. In the highly significant districts, development activities should require special attention to assess their environmental impacts. In contrast, for the least significant districts a set of indicators can be identified and shared with the District Governments to improve and monitor their ecological conditions.