The main problem faced in the national park by the endangered species is the illegal hunting and the hybridisation with the free ranging domestic goat (furiarico). Additionally, although to a lesser extent is the disturbance of the natural habitats and the competition with the domestic species.
One of the rarest representatives of the Greek fauna constitutes the Cretan wild goat or Agrimi (Capra aegagrus cretica Schinz 1938) which is endemic to the island of Crete. Recently the animal reached the limits of extinction leading to the establishment of a legal status by the Crete public authorities. Although currently it is strictly protected by Greek legislation, it is considered an endangered species. In the past, when habitat disturbance was not so intensive and long range hunting rifles not as common, the animal was living in natural populations in many regions of Crete. Today the only naturally occuring population of Agrimia is found in the vicinity of the Samaria gorge and neighboring gorges of the Samaria National Park. There is an estimate of about 600-700 wild goats in total.