Christian women light candles during a Mass held for three men killed in the predominately Christian village of Maalola, at al-Zaytoun Church for the Roman Catholic in Damascus. (Youssef Badawi/EPA)

When radical Islamists tore down a cross and hoisted a black flag above a church in the northern Syrian city of Raqqah last week, their action underscored the increasingly hostile environment for the country’s Christians.

Although Syria is majority Sunni Muslim, it is one of the most religiously and ethnically diverse countries in the Middle East, home to Christians, Druze, and Shiite-offshoot Alawites and Ismailis. But the country’s conflict, now in its third year, is threatening that tapestry.

While the primary front in the war has pitted Sunni against Shiite, Christians are increasingly caught in the line of fire. The perception that they support the government — which is in many cases true — has long made them a target of rebel groups. Now, Christians say radical Islamist groups such as the Islamic State of Iraq and Syria (ISIS), an affiliate of al-Qaeda, are determined to drive them from their homes.

“The Christian community in Syria is stuck between two fires,” said Nadim Nassar, a Syrian from Latakia who is director of the Awareness Foundation, an interfaith charity based in Britain. “One fire is a corrupt regime, and everybody agrees there needs to be a change. And on the other hand, there’s a fragmented and diverse opposition on the ground who can’t control jihadist forces coming from outside the country.”

Syria is not the only place in the wider region where Christians are being targeted. Coptic churches in Egypt have been attacked, and Pakistan last week experienced the deadliest church bombing in the country’s history. The militants who attacked a mall in Nairobi last month singled out non-Muslims.

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The rash of assaults has led some to question the future of Christianity in Syria, where adherents make up about 10 percent of the population, and in the wider Middle East.

Syria’s ruling Assad family, which belongs to the Alawite sect, has long painted itself as the protector of Syria’s minorities. Though leaders of Syria’s opposition have pledged to provide minorities with equality in a new Syria, they are unable to control the growing number of hard-line Islamist forces on the ground.

The Western-backed Syrian Opposition Coalition denounced the desecration of the churches in Raqqah, calling it an act that showed “complete disregard to holy sites and religious and cultural heritage.”

But the rejection of the opposition coalition by 13 rebel factions that announced an Islamic alliance last week highlighted the group’s lack of influence.

In Syria’s war, bishops have been kidnapped and priests have been killed. When the fighting last month reached the ancient town of Maaloula — where residents still speak Aramaic, the language of Jesus — it struck at the heart of Syria’s Christian community.

Most residents have fled since rebels swept through the picturesque town, which clings to the mountains northwest of the capital, Damascus.

“Maaloula is like Jerusalem to Syrian Christians,” said Ibrahim Doushi, a Syrian Christian shop owner who moved to neighboring Lebanon. “When the war reached there, it was heartbreaking for all the Christians in the Middle East.”

The fighting in Maaloula was followed by the images from Raqqah, where the ISIS desecrated the Greek Catholic and Armenian Catholic churches, according to activist groups. The radical Islamist group also has attacked Shiite shrines and mosques.

For Doushi, who fled to Lebanon last year from the town of Ras al-Ayn, near the Turkish border, the footage of the ISIS’s black flag flying above the Armenian church was confirmation that he and his family have no future in his home country.

“Christians are being torn from our roots,” he said. The ISIS militants “are proud of it. They are targeting the Christians and they are publicizing it. The regime cannot protect us.”

Doushi said he was forced to leave Ras al-Ayn after Islamist fighters entered the town late last year and targeted the homes and businesses of Christians. The 61-year-old’s new, temporary residence, housing seven members of his extended family, is St. Gabriel’s monastery in the mountain village of Ajaltoun, 12 miles north of Beirut.

Many at the monastery say they are pinning their hopes on obtaining European visas, citing doubts that there will ever be a day that Syria can offer security to its minorities, at least in rebel-held areas.

“The Christians are never going back,” said Johnny Chamoun, 42, also from Ras al-Ayn, who works at the monastery coordinating assistance for Syrian Christian refugees.

Nassar, the interfaith foundation director, said it is the first time in centuries that Christians in Syria have been targeted for their faith.

“We are not imported there. Christ was not born under Big Ben or in Paris,” he said. “This is the cradle of Christianity that we are being pushed from.”