Some saw a symbolism in the unusual collision, as the protesters intruded into the Kremlin-backed holiday, forcing most those who had come to enjoy the authorized event to disperse. "People 30 or older, they have more to lose if they get arrested". He was arrested at his home in Moscow roughly an hour before it was due to start.
Navalny was also behind the massive protests organized in March. Then, on March 26, tens of thousands of people turned out across Russian Federation for an "anti-corruption" protest. In Moscow, thousands of angry protesters held an unsanctioned rally on the capital's main street with riot police snatching hundreds of protesters from the crowd at random.
A White House spokesman said the United States condemned the detentions.
The Moscow city government had previously approved the protest to be held in a square just outside the center.
While 4,500 people came to Tverskaya Street to participate in the unauthorized protest, over 270,000 people visited the central Moscow street to take part in the Russia Day festivities, according to police estimates.
The demonstrators are demanding an end to corruption they say is endemic among government officials.
Navalny, who was also detained at a similar protest in March, has sought to challenge Putin in next year's presidential election, but he appears unlikely to be allowed on the ballot because of a controversial past conviction on corruption charges.
Navalny was among those arrested Monday.
Russia's biggest problem is that people don't believe they can change anything, he said, so the government feels free to do whatever it wants.
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Instead, he urged demonstrators to gather on Tverskaya Street, a main Moscow avenue that was closed to traffic for a celebration of the national Russia Day holiday that included people dressed up in various costumes from the country's history. We saw dozens of people plucked from the crowd - many of them young - and dragged roughly towards police buses.
A protest in March against alleged corruption linked to the Prime Minister, Dmitry Medvedev, drew an estimated 60,000 people to the streets in cities across Russian Federation.
Teenagers were seen crafting signs in the streets, the AP reported.
Witnesses saw a police vehicle leaving Mr Navalny's apartment compound at high speed, followed a few minutes later by a minibus carrying around 10 police officers. "There is no intention to mop up everyone, but targeted professional work is under way in relation to those who are continuing to provoke the situation", commented the Moscow security department.
In a call for people to join him on Monday, Mr Navalny wrote: "I want changes". He said interference had prevented contractors from building a stage at the agreed venue.
It's a tall order but there's no question Navalny has touched a nerve.
Attendees chanted phrases including "Russia without Putin", "Putin is a thief", and "we deserve an honest Russia".
The protests in March were called to demand the resignation of Prime Minster Dmitry Medvedev.
A protestor being led away by the police on Monday summed it up. There was no immediate statement from police.
Police in the capital have put on gas masks and witnesses say pepper spray has been used against some protesters.
A series of anti-government protests against corruption and political stagnation led by the Opposition swept through Russian Federation on Monday, leading to the arrest of thousands of demonstrators including Opposition leader Alexei Navalny who has been sent to jail for 30 days. Other protests were in Vladivostok, Khabarovsk and in Barnaul, Siberia.
The prosecutor's office has warned police will take action against any unauthorised demonstrations. Mass arrests followed on the day of the rally.