A senior Jordanian military official confirmed the pilot was seized, saying his plane went down in Syria's Raqa region, a militant stronghold, early today.
"The pilot was taken hostage by the IS terrorist organisation," official news agency Petra quoted the official as saying.
Jordan did not say why the plane went down, but both the jihadists and a monitoring group said it was shot with an anti-aircraft missile.
If confirmed, it would be the first coalition warplane shot down since air strikes on IS began in Syria in September.
Coalition warplanes have carried out regular strikes around Raqa, which IS has used as the headquarters for its self-declared "caliphate" after seizing control of large parts of Syria and Iraq.
The IS branch in Raqa published photographs on jihadist websites purporting to show its fighters holding the captured pilot.
One showed the pilot, wearing only a white shirt, being carried from a body of water by four men. Another showed him on land, surrounded by about a dozen armed men.
The jihadists claimed to have shot down the warplane with a heat-seeking missile.
The pilot's father Youssef was quoted by Jordanian news website Saraya as saying the family had been informed by the air force of his capture.
He said the military promised it was "working to save his life" and that Jordan's ruler, King Abdullah II, was following events.
Jordan is among a number of countries that have joined the US-led alliance carrying out air strikes against IS.
Australia, Belgium, Britain, Canada, Denmark, France and The Netherlands have joined the raids in Iraq.
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