With helmeted riot police looking on, some 10,000 protesters chanted "Russia without Putin!" and called for the release of activists who face long jail terms over violence at a protest against his inauguration to a third presidential term last year.
Critics accuse Putin, in power since 2000, of clamping down on dissent after he weathered the biggest protests of his rule and returned to the Kremlin following a stint as prime minister.
"We have no democracy here, we have what Putin calls sovereign democracy. That means there is democracy for them, not for us," said protester Andrei Rusakov, 53.
Protesters chanted "Putin is a thief" and held pictures of 12 activists who are being tried over clashes with police at a rally the day before he was sworn in.
A bridge leading across the Moscow river toward the Kremlin was blocked by police lines, bulldozers and water trucks. Police said they detained nine members of a suspended opposition group.
Shortly after the march, Putin, 60, was chosen to lead the Popular Front at a highly choreographed congress of the group he created in 2011 as a source of support to supplement the ruling United Russia, which many Russians mistrust.
In a spectacle that mixed elements of Soviet Communist Party meetings and Western-style political conventions, members chanted Putin's name after a speech full of patriotic rhetoric.
"We are united by values that are higher than political passions," Putin told the gathering, which included cultural and religious figures, stylish young women and medal-bedecked World War Two veterans.
Putin spoke of freedom, human rights and the rule of law in his address but protesters said he has trampled on those values since starting his six-year third term.
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Putin has signed laws restricting demonstrations and labeling U.S.-funded civic groups "foreign agents". Protest leaders are under investigation or on trial in what they say are trumped up charges.
Marchers, hoping to revive flagging protests, focused on the plight of 12 lesser-known activists who face up to eight years in jail over clashes with police in what critics call a Stalin-style show trial meant to scare away ordinary Russians.
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"This is a political trial ... it is all clearly falsified," said Natalya Kavkazskaya, whose son Dmitry, 26, is among the defendants and has been in pre-trial detention since last July.
"Mother Russia is in tears, crying like all mothers over their children in this country," she said at the protest, which took place on a holiday called Russia Day.
More than half of Russians polled by the independent Levada Centre last month said the case was meant to intimidate Putin's foes.
Some posters targeted Putin's announcement last week that he and his wife Lyudmila were divorcing: "He wants someone else — and so do we."
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Putin remains Russia's most popular politician by far, but his job approval rating fell to a 12-year low of 62 percent in January, according to Levada Centre.
"We want the authorities to stop fabricating criminal cases against opposition leaders and activists," Dmitry Gudkov, an opposition lawmaker and protest leader.
"Those in power are not changing but society is, and if the authorities do not catch up with that the same thing will happen to them as with leaders in some Arab countries," he said.
While the protests have waned, they exposed fatigue with Putin an dissatisfaction with the dominance of United Russia, his main source of support and instrument of power.
Opposition leaders have dubbed it the "party of swindlers and thieves" and its majority in parliament was cut sharply in the December 2011 election that set off the wave of protests.