When the Arab Spring reached Syria last year, it dredged up animosities that had been lurking for decades. The protest movement was avowedly nonsectarian, attracting Syrians from all communities. But in the government’s eyes, the opposition was simply a Sunni front seeking to topple the Assad family and end Alawite rule.

The Syrian government’s actions have deepened the sectarian divide. As the violent repression of protests gave way to the destruction of opposition-controlled villages, the government moved from targeting individual dissenters to imposing collective punishment upon entire neighborhoods. Sunni areas were shelled by artillery and tanks, and the pro-government shabiha militia, made up mainly of Alawites, carried out ferocious massacres of men, women and children. The majority of victims were Sunni civilians.

As the civil war intensifies, Mr. Assad is increasingly outsourcing the dirty work. In Damascus, militia groups within Druse, Christian and Shiite areas are being armed by the government. While the justifications for these militias are “neighborhood self-defense” and the protection of religious sites, the shabiha emerged in a similar way before becoming killing squads for Mr. Assad. And by drawing Christians, Druse, Shiites and Alawites into the civil war on an explicitly sectarian basis, the Syrian government has all but guaranteed that there will be reprisals against these communities if Mr. Assad falls.

Indeed, as pro-democracy protests degenerated into civil war, the ideological composition of the opposition changed. The Free Syrian Army’s slogan remains, “We are all one people of one country.” But inside Syria those chanting “Christians to Beirut, Alawites to their graves!” have become more than a fringe element. Human Rights Watch and other groups have documented cases of rebels executing Syrian soldiers and Alawites regarded as government collaborators.

Growing numbers of foreign Sunni extremist fighters are battling not just to rid Syria of Mr. Assad, but to religiously cleanse it. As a result, many Syrian Christians now fear that their fate will mirror that of Iraqi Christians, who were largely forced out of Iraq by war and sectarian terrorism. The city of Homs was once home to 80,000 Christians; there are now reportedly fewer than 400.