"The truth is that we need to get ready for a long and more difficult struggle," he said.
In July, Navalny was convicted of embezzlement and sentenced to five years in prison on charges widely seen as political, but he was released the next day in what some saw as a government attempt to make the Moscow mayoral race, in which he took part, look more competitive.
Navalny won 27 percent of September's vote, finishing a strong second behind the Kremlin-backed incumbent. The surprisingly strong performance cemented his positions as the No.1 Russian opposition politician.
Earlier this month, a court replaced a prison term for Navalny with a suspended sentence.
The protesters carried pictures of those who are on trial for their role in the May 2012 protest that turned violent. Some also held pictures of former oil tycoon Mikhail Khodorkovsky, who marked 10 years in prison this week since his arrest on charges widely seen as a punishment for challenging Putin's power.
Some people carried pictures of the two members of the punk band Pussy Riot, who are serving two-year sentences for an irreverent protest against Putin. One woman carried a colorful umbrella with the images of masked Pussy Riot performers.
After Putin's inauguration, the Kremlin has sought to stifle dissent with a series of arrests of opposition activists and repressive legislation that sharply hiked fines for participants in unsanctioned protests and imposed tough new restrictions on non-government organizations.
"We want to show the government, the Russians, the global community yet another time that Russia is not a democratic country, but is governed by the police," rally organizer Vitaly Zalomov said.