Francis encourages believers in the region to be proud of their Christian heritage despite the "the continuing hostilities in the region, but especially because of the work of a newer and disturbing terrorist organisation."
Though the Pope does not refer to the organisation by name, Islamic State militants in recent months have forced hundreds of thousands of Christians, Yazidis and other minorities from their homes and villages in Iraq.
"Do not be afraid or ashamed to be Christian. Your relationship with Jesus will help you to cooperate generously with your fellow citizens, whatever their religious affiliation," Francis said in his letter.
"Within the region you are called to be artisans of peace...in a spirit of ready cooperation with all national and international authorities.
"In a special way I would like to express my esteem and gratitude to you... who accompany the journey of your communities with loving concern.
"How valuable is the presence and work of those completely consecrated to the Lord, serving him in their brothers and sisters, especially those in greatest need"
The Pope's message has come as the Jordanian military confirmed that one of its planes has crashed over northern Syria and that its pilot has been captured by Islamic State (IS).
The jihadist group earlier said it had shot down the jet with a heat-seeking missile near the city of Raqqa.
It published photographs showing the pilot, whom it identified as Flight Lieutenant Moaz Youssef al-Kasasbeh.
This is the first US-led coalition aircraft to be lost on IS territory since air strikes began in September.
Emma Loosley, Associate Professor of Middle Eastern Christianity at Exeter University, told Premier's 'News Hour' that Lebanon now remains the only safe haven for Christians in the Middle East, she said: "It's only the Christian community of Lebanon who are perhaps feeling that they have any future at all. Even many Lebanese are feeling very very threatened by this, because of destabilisation of refugees from Syria. They're scared that Lebanon could get sucked into what's going on around them."
Emma Loosley, Associate Professor of Middle Eastern Christianity, Exeter University:
