Navalny, who is President Vladimir Putin's most prominent and determined foe, was returning from Germany, where he spent five months recovering from poisoning by a nerve agent, which he blames on the Kremlin.
Navalny was taken to Germany five months ago in a coma after being poisoned with Novichok, a military-grade nerve agent developed by Russian Federation during the Soviet years. The Kremlin denies involvement.
Footage from the airport showed Mr Navalny kissing his wife goodbye as he was arrested and led away.
His supporters gathered at Moscow's Vnukovo airport despite a forecast of bitterly cold minus 22 Celsius weather and over 4,500 new coronavirus cases a day in the Russian capital.
In a case that drew wide worldwide attention, Navalny was poisoned last summer by what German military tests showed was a Novichok nerve agent, a version of events the Kremlin rejects. "On January 17, Sunday, I will return home on a Pobeda flight", he said in a tweet on January 13, referring to a Russian airline whose name means Victory.
Back in December, the country's Federal Penitentiary Service (FSIN) warned that Navalny would face time in prison if he failed to report to its office line with the terms of a suspended sentence and probation he received for a 2014 conviction on charges of embezzlement and money laundering.
OVD Info, which monitors detentions at political protests in Russian Federation, said at least 37 people had been detained at the airport.
Russian Federation issued an arrest warrant for Navalny after accusing him of violating the conditions of a 3½ year suspended fraud sentence by not appearing in person for regular summons.
Russian opposition leader Alexei Navalny and his wife Yulia Navalnaya on their flight to Moscow on Sunday | REUTERS
He had spent almost the last five months recovering in Germany after being poisoned in August.
The Kremlin had ordered Navalny to return saying his continued stay in Germany, where were was flown in a coma in August, breached a suspended jail sentence against him.
There has already been an outpouring of support for Navalny, and Jake Sullivan - incoming national security adviser for Joe Biden - called for him to be "immediately released".
The EU's foreign policy chief Josep Borrell echoed the call for Navalny to be freed following his arrest, which came as the anti-corruption campaigner returned to Moscow for the first time since his poisoning in August.
Italian Economy Minister Roberto Gualtieri on Twitter also asked for Navalny's immediate release.
They refused to open a fully-fledged criminal inquiry, citing a lack of evidence that Mr Navalny had been poisoned.
The FSB dismissed the recording as fake.
Opposition activist Alexei Navalny's wife Yulia (C) is seen at the Sheremetyevo International Airport after arriving with her husband from Berlin.
Lithuania's Foreign Minister Gabrielius Landsbergis has called for European Union sanctions against Moscow, while Amnesty International accused Russian authorities of waging "a relentless campaign" to silence Navalny.
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