Marchers at the event which attracts nationalists and skinheads shouted slogans including "Putin is a thief" and and "Freedom for political prisoners."
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Police in helmets and body armour moved in to seize activists, mostly young men, at the authorised event in Lyublino in southern Moscow.
The detentions came after police banned demonstrators from bringing in banners bearing slogans. Organisers then formally called off the march.
More than 30 people were detained, a law enforcement source told TASS state news agency. Police have not yet given a figure.
OVD Info, which monitors detentions of political activists, said 41 people were held, including an organiser, Konstantin Filin.
Another organiser, Party of Nationalists leader Ivan Beletsky, told Interfax news agency that more than 70 were detained.
He wrote on Facebook that police searched his family's flat ahead of the march, while he was not at home.
The Russian March is an annual event held with official authorisation that gathers various protest groups of nationalists and skinheads.
This year, police said around 200 people attended, while an AFP journalist put the number at 300.
"We are against the tyranny of (President Vladimir) Putin's regime of occupation, which we don't recognise at all," said one young protester from a group called the Black Bloc, who gave his name only as Artyom.
"The Russian March comes out to show that our rights are being violated," said Dmitry Golikov, spokesman for the Party of Nationalists, which claims ethnic Russians are experiencing a "genocide".
The nationalist movement has split in recent years, with some backing the Kremlin's annexation of Crimea while others oppose Putin.
Since Putin's return to the Kremlin in 2012, Russia has cracked down on nationalist leaders, many of whom are jailed or living in exile.
Opposition leader Alexei Navalny, who has espoused some nationalist views, was a speaker at previous Russian Marches, most recently attending one in 2011.
He has announced he intends to stand for the presidency in 2018 but the authorities say he is ineligible due to a fraud conviction.
This year, nationalists held two separate marches in Moscow due to disagreements between organisers.
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