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Emmanuele, 43 was "driving alone when attackers opened fire on his vehicle" on the road between Goma and the Virunga National Park headquarters.
Goma is described as "war-torn eastern Congo's main city."
The Virgunga National Park is home to about a quarter of the world's "880 remaining critically endangered mountain gorillas.
Pine Emmanuele was rushed to a Goma hospital, where surgeons removed several bullets from his chest
"He's stable now and doing much better than he was yesterday," said Joanna Natasegara, spokeswoman for the Virunga National Park. "There were two or three bullets that were taken out, so obviously we're still worried. But he's being his usual strong self."
No one has claimed responsibility for the attack, but, according to the Daily Telegraph, Prince Emmanuel "has made enemies of armed militias and poachers" during his six years as director of Virunga, which is Africa's oldest reserve.
Prince Emmanuel, 43, is married to Louise Leakey, daughter of the Kenyan conservationist, Richard Leakey.
Prince Emmanuel Werner Marie Ghislain de Merode was born at Carthage on, Tunisia, on May 5, 1970. He is the second son of Charles Guillaume, Prince de Merode, and Princess Hedwig de Ligne.
He married Louise Leaky in a civil ceremony in Nairobi, Kenya, is December 2003. A religious ceremony at Serrant took place in May 2004. Princess Seiya was born at Nairobi on August 31, 2004. Princess Alexia was born at Nairobi in September 2006.