Images and videos from the site, verified by BBC, show armed men walking around the burning mausoleum in Qardaha, in the northwestern part of the Latakia coastal region.
Other family members' graves are also located at the site, including Bashar al-Assad's brother Bassel, who was on his way to inherit power before he died in a traffic accident in 1994.
Hafez al-Assad ruled the country from 1971 until his death in 2000, when his son Bashar took over power.
The rebels, led by the Islamist movement Hayat Tahrir al-Sham (HTS), seized power in Syria on Sunday in an offensive that toppled the al-Assad family's long-standing rule. Bashar al-Assad has fled to Russia, where he and his family have been granted asylum.
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