The Syrian Observatory for Human Rights said the bodies of at least nine detainees had been found after the northwestern city was overrun by a coalition of forces including Al-Qaeda's Syrian affiliate Al-Nusra Front.
"The bodies of nine people believed to have been killed by regime forces before Idlib's capture were found at a detention centre," the Britain-based group said.
Al-Nusra meanwhile released video on Twitter showing fighters from the group discovering the bodies in a prison in Idlib.
It was unclear how the men had been killed.
The discovery came after a coalition of Islamist fighters seized full control of Idlib yesterday, on the fifth day of fighting for the city.
The grouping, known as the Army of Conquest, brings together jihadists from Al-Nusra with Islamist allies including the powerful Ahrar al-Sham organisation.
The capture of Idlib makes the city only the second provincial capital in Syria to have fallen from regime control, after the March 2013 loss of Raqa city.
IS has since made the city the de facto Syrian headquarters of the Islamic "caliphate" it has declared in territory under its control in Syria and Iraq.
With Idlib's capture, Al-Nusra and its allies control most of the northwestern province, though regime forces maintain a presence in two additional cities, as well as the Abu Duhur military airport and several military bases in the region.
Last November, Al-Nusra and allied forces ousted a series of Western-backed rebel groups from Idlib after announcing plans to establish an Islamic "emirate" that analysts say is intended to rival IS's "caliphate".
Without making reference to the composition of the forces that captured Idlib, the Coalition said it had "confidence" that they would protect civilians and abide by international law.
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