The Nabi Yahya Mosque stands on the site identified since Byzantine times as the place where John the Baptist's body was buried by his followers.

In 1870, the French explorer Victor Guérin visited the place, and noted: At the western extremity of the monument rises a Musulman sanctuary crowned by a little cupola pierced with narrow windows, which admit a feeble light into the crypt which it covers.

Here lies the door of which I have just spoken: mouldings divide it into compartments; it is provided with hinges worked in the thickness of the block which composes the stone.

This crypt, of small extent, contains a sepulchral chamber divided into three parallel arched loculi, with cut stones regularly worked between them.

[2] Local tradition in both the Christian and Muslim communities of the area notes that Sebastia also contained the site of the prison of John the Baptist and is the place where he was beheaded; however this was a separate church in the old city and is a claim refuted by the account of the first century historian Josephus, which recorded the site of the beheading as Machaerus, across the Jordan, some 80–90 miles (130–140 km) away.