Alexei Navalny, a vocal critic of President Vladimir Putin, was detained as he made his way to a planned anti-Kremlin rally in the heart of the Russian capital.
Police say he is going to be charged with failure to follow police orders and could be sent to jail for 15 days.
The 41-year-old had called for mass protests nationwide against corruption, with anti-graft demonstrations planned in more than 180 towns and cities.
A photo of Mr Navalny being bundled into a police car was posted on Twitter by his wife Yulia, who said the protests were going ahead nonetheless.
The activist's spokeswoman also confirmed that electricity had been cut at his office - temporarily disrupting an online feed of nationwide demonstrations.
At least 200 people are believed to have been detained in the anti-corruption protests across Russia so far.
Dozens of protesters were held in the centre of St Petersburg, and more than 50 of Mr Navalny's supporters were arrested by riot police near Pushkin Square in Moscow.
As demonstrators were taken away, hundreds of others shouted slogans including "Putin is a thief" and "Shame!".
Police in the capital have put on gas masks and witnesses say pepper spray has been used against some protesters.
Mr Navalny angered officials in Moscow after he made a last-minute decision to change the main protest's location to one of the city's busiest thoroughfares.
The leader had been given permission to hold a rally away from the city centre, but claimed Russian authorities had pressured companies into refusing to supply him with sound and video equipment.
Before the protest began on Tverskaya Street, a stone's throw away from the Kremlin, prosecutors warned the rally was illegal and police would take "all necessary measures" to prevent disorder.