Syria. Christians believe that they will have no place in Syria if Mr. Assad leaves power.

More than 19,000 people, most of them civilians, have been killed since March last year, in violence in Syria since the outbreak of an anti-regime revolt last year, the Syrian Observatory for Human Rights said on Sunday.

ZAHLEH, Lebanon—Syria’s conflict, increasingly characterized as a Muslim sectarian war, is now also threatening to engulf the country’s estimated 2 million Christians.

As clashes between government forces and rebels spread over the weekend from the capital Damascus to the northern city of Aleppo—Syria’s two largest urban centers that are home to sizable Christian communities—the Christians and other minorities are being forced to take sides.

Several Christian residents and antiregime activists in Damascus say the regime is now arming male loyalists in parts of the capital dominated by Christians and Druze and Shiite minorities.

Syria’s conflict has until now largely played out between supporters of President Bashar al-Assad—whose minority Shiite-linked Alawite sect makes up the core of his security apparatus—and an opposition dominated by Sunni Muslims, estimated to make up 70% of the country’s 23 million people.

Christians account for nearly 10% of the population. They have generally remained neutral or stood by the Assad regime, which has characterized itself as a secular government holding together a nation of diverse faiths.

On Sunday, opposition activists in the capital said government troops conducted raids in several Damascus districts where rebel fighters have been active for more than a week. In Aleppo, residents said government forces laid siege to the Salahuddin neighborhood after they clashed with rebels there over the weekend giving residents the chance to leave and rebels an ultimatum to surrender.

They say at least 200 Russian-made AK-47s have been handed out in one Christian neighborhood in Old Damascus since Thursday, a day after a bombing killed four top regime officials including the defense minister Gen. Dawoud Rajha, a Christian. A recent wave of kidnappings, intimidation and revenge killings in the town of Qusayr, in an area of Syria where religious groups have lived side by side for centuries, provides a cautionary example of what may lie ahead for other heavily Christian areas particularly in urban centers.

On Saturday Brig. Gen. Nabil Zougheib, a Christian missiles expert, was assassinated along with his wife and son at their home in a Damascus Christian neighborhood, activists and state media said. Many Christians believe they are being targeted for being mostly with the regime.

Qusayr’s conflict was sparked when some local Christians acted as informants to Mr. Assad’s security apparatus, said several Sunni Muslims from the area. In the months since, several men from a prominent Christian family have been shot dead, more than a dozen residents have gone unaccounted for and the majority of Christians have fled town, said residents on both sides of the conflict.

“The situation is worsening. People are rejecting each other,” said a Syrian Christian priest from the western city of Homs, who attended an interfaith meeting in Geneva in mid-July that brought together Christian, Alawite and Sunni religious leaders in a bid to stave off intercommunal violence.

Those risks appear to be spreading. In an enclave of some 30 villages west of the city of Homs known as Wadi al-Nasara—the Valley of Christians—a family of pro-regime Christians has taken up arms alongside Alawite loyalists, say residents who recently fled the area.

And now many fear the same dynamic is playing out in major cities where the regime is starting to arm loyalist civilians from minority groups.

“The slightest skirmish and we are going to be part of the bloodbath,” said an antiregime Christian activist from Damascus who says she is the odd one out in a family of staunch Assad supporters.

Qusayr lies southeast of the city of Homs, less than 10 miles from the Lebanese border.

The provinces of Homs and adjacent Hama, collectively known as the Orontes River Valley, have been the epicenter of Syria’s sectarian civil conflict.

The accounts of Qusayr’s troubles were provided by more than a dozen people from the town, including Muslim fighters and members of a prominent Christian family now taking refuge in the eastern Lebanese city of Zahleh across the border.

Tensions started more than a year ago, after early protests against Mr. Assad’s regime turned violent. Government forces started raiding Muslim homes, these people said, arresting suspected antiregime activists and protesters.

Pro-regime residents, many of them Christian, helped government security forces, opposition fighters and residents say.

“If you went out to protest, they would write down your name and send a text message to security forces,” said Mahmoud Harba, 25 years old, a Sunni rebel from Qusayr hospitalized after losing a leg in the fighting.

The worst offenders, he and other Muslims from the town said, were members of the pro-regime Kasouha clan, which is prominent among the 10,000 Christians in the town of 60,000.

Rebels retaliated against the suspected informants last summer by killing one of the family’s three adult brothers, Muslim regime opponents and Christians from Qusayr say.

The murdered man’s brother, Hanna Kasouha, erected a security checkpoint next to his home and took up arms, aided by government forces, these people said. Syrian authorities couldn’t be reached to comment.

One photo Mr. Kasouha on a relative’s mobile phone shows a heavyset, bearded man dressed in military fatigues.

Many local Muslims, meanwhile, had joined the ranks of antiregime fighters. Among them are an increasing number of Sunni Muslim fundamentalists who see the conflict as a holy war. Members of Mr. Assad’s Alawite minority are infidels who should be wiped out, according to this view, which is barely more tolerant of Christians.

“All Alawites must be slaughtered,” said Hassan Harba, 30, a Sunni Muslim rebel fighters who was being treated recently at a hospital in Lebanon for wounds sustained during fighting with pro-government forces. He isn’t against Christians, he said, but against those who help the regime in its brutal crackdown on the opposition. “The informant must die,” Mr. Harba said.

After Mr. Kasouha set up the checkpoint with the help of security forces, Muslim rebel fighters kidnapped Mr. Kasouha’s uncle, according to both sides.

Mr. Kasouha then organized the kidnapping of eight local Muslim men, these people said.

Several times during the height of the crisis, in February, loudspeakers from mosques in the town told Christians they should leave the town, say both Muslims and Christians.

Town elders on both sides of the dispute negotiated a hostage exchange in late February, the Christian resident said. As part of the deal, Mr. Kasouha said he would leave.

Instead, he evacuated his mother and surviving brother, before returning to town and hiding out in his home’s cellar, relatives say. When Sunni rebel fighters went to the home, he attacked them. The fighters returned to the home two days later and killed Mr. Kasouha and his father in a gunbattle, according to Christian and Muslim residents.

Christians began leaving town, joining a broader flow of Muslims and others who have relocated within Syria or fled abroad. Several more remain unaccounted for. The Christians from Qusayr name brothers, cousins and other relatives who they say are among more than a dozen Christians from the community whose fate remains unknown.

In late May, an Italian Jesuit priest working in Syria, Father Paulo Dall’Oglio, spent eight days in Qusayr at the request of Christian families to help locate about a dozen missing relatives. Toward the end of his stay, Father Dall’Oglio said in an interview, he met with some of the most influential and militant rebel factions in Qusayr, who he described as Syrian men wearing long beards and Afghan-style traditional dress.

He secured the release of two of them, he said, but concluded that the rest were “most probably killed.”

Father Dall’Oglio, who spent three decades in Syria, was expelled in June after expressing sympathy with the opposition’s democratic aspirations. He attributes the cycle of violence in Qusayr to hardened views on both sides that he says don’t represent those of most Syrians.

On one side, he said, Mr. Kasouha and some of his family took extreme actions—while on the other, he said, the mostly Sunni opposition features an ultraconservative, militant fringe that the opposition has no power to control.

Some Sunni Muslims say they believe reconciliation is possible with those who have sided with the regime.

“We have nothing against the Christians and Alawites,” said Mohammed Idriss, 30, a farmer and taxi driver who also fled the area. “It’s just the vile regime that has exploited this.”

Few Christians from Qusayr share his optimism. The Christian men in Lebanon believe that Christians will have no place in Syria if Mr. Assad leaves power—saying that the recent animosity has uncovered the true feelings their former neighbors had kept hidden for years. “We ate from the same plate,” said one of the displaced Christians. “And then they stabbed us in the back.” (WSJ)