They did the same at the Armenian Catholic Church of the Martyrs, and also destroyed a cross atop its clock tower, replacing it with the ISIL flag, the Observatory said.
Most of Raqa, located on the banks of the Euphrates River and capital of the province of the same name, fell to anti-regime fighters in March.
Where the ISIL dominates in the city, it imposes a strict version of sharia (Islamic law) on the populace.
The London-based Observatory denounced these attacks “against the freedom of religion, which are an assault on the Syrian revolution.”
Not only have there been attacks on Christian places of worship in Syria, a predominantly Sunni Muslim country wracked by more than two years of civil war, but also on Shiite Muslim mosques.
Additionally, Christians clerics have been kidnapped, and some brutally murdered, by jihadists.
In January, the Middle East director of Human Rights Watch, Sarah Leah Whitson, said: “The destruction of religious sites is furthering sectarian fears and compounding the tragedies of the country.
“Syria will lose its rich cultural and religious diversity if armed groups do not respect places of worship.”
The New York-based group said that “while some opposition leaders have pledged to protect all Syrians, in practice the opposition has failed to properly address the unjustified attacks against minority places of worship.”
At the outset of the rebellion against President Bashar al-Assad, rebels welcomed the support of jihadist groups, largely made up of foreign fighters.
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Agence France Presse