In 2000, Mexico’s National Commission of Protected Areas (CONANP) was created to encourage the protection, management and restoration of natural and cultural resources and their conservation. Protected areas were recently increased by more than 3 million hectares, for a current total of more than 25 million hectares, corresponding to 174 protected areas that cover 12.90% of the country’s surface area. The information obtained by research helps us understand both biodiversity and ecological processes, as well as the social and economic phenomena that influence the use of ecosystems. In Mexico there are four species of deer: white-tailed deer, mule deer, red brocket and brown brocket. These ungulates have been an important part of the diet of indigenous people and rural communities, and represent an important resource for sport and trophy hunting. We found the best deer populations in protected areas; these can therefore maintain the gene pool and serve as source populations for other areas. These populations are also useful from a research perspective. People living in some protected areas continue to use natural resources such as deer, and also receive economic inputs to develop ecotourism programs, and support from the government for the environmental services derived from conserving biodiversity.