“While they are in a cage, we are all in a cage,” Mr. Navalny said as the crowd called for freedom for “political prisoners.”
Mr. Putin has denied that a “clampdown” is under way.
“If we understand this term as a simple requirement that everyone, including the opposition, complies with Russian law, then this requirement will be consistently enforced,” he said earlier this month.
The rally took place a day after the parliament expelled outspoken lawmaker Gennady Gudkov over alleged illegal business activities. Mr. Gudkov is the second lawmaker ever to be ousted from the lower house without a court decision and now could face prison time after losing his parliamentary immunity from prosecution.
Mr. Gudkov, a former KGB officer like Mr. Putin, said last week that his expulsion was “political payback” for his involvement in the protest movement. Ahead of his ouster, he warned lawmakers from the ruling United Russia party that he would return to parliament to “help build a new country.”
“We have no constitution, no law and no parliament worthy of the name,” Mr. Gudkov said Saturday after he was introduced on the rally stage as “one of Russia’s future leaders.”
“The authorities must compromise or we will overthrow them,” he said to loud applause. “But we must be united.”
Although Mr. Putin’s approval ratings are falling, his figures remain high by Western standards, and anti-Kremlin rallies held in other cities across Russia on Saturday failed to draw significant numbers.
Mr. Putin, who turns 60 next month, has shown little sign that he is willing to negotiate with protesters, whom he described last year as Western-backed, chattering monkeys.
With no nationwide elections due until 2016, protest leaders have turned their attention to regional polls, and the immediate focus is on high-profile ecological activist Yevgenia Chirikova’s bid to become mayor of the Moscow satellite city Khimki.
“Elections are an excellent chance to work with people,” Ms. Chirikova said Saturday. “We need to make people understand that they can change things, that they can make a difference.”
Ilya Yashin, leader of the Solidarity movement, said at the rally that the opposition needs to demonstrate “discipline and organization” if it is to succeed.
“People need to see the results of our work,” he said.