The development comes just days after a Russian citizen pleaded guilty to meddling in domestic politics in the United States.
Russia's domestic security agency said on Monday it has arrested a US citizen on espionage charges.
The Federal Security Service, or FSB, said that the American man detained in Moscow on Friday.
The agency said in Monday's statement that he was caught "during an espionage operation," but didn't give any details.
The state Tass news agency identified the detained man as Paul Whelan. Spying charges carry a prison sentence of up to 20 years in Russia.
The US Embassy in Moscow had no immediate comment.
The arrest comes as Russia-US ties have sunk to post-Cold War lows over the Ukrainian crisis and the war in Syria.
US intelligence services have accused Moscow of interfering in the 2016 presidential election and earlier this month convicted Russian Maria Butina of acting as an illegal foreign agent.
Butina faces up to six months in prison, followed by likely deportation.
Prosecutors said she launched a plan in March 2015 to develop ties with the Republican Party with the aim of influencing US foreign policy.
Russian military intelligence agents were also accused in the poisoning earlier this year of former double agent Sergei Skripal and his daughter in Salisbury, England.
Relations between Russia and the West have hit a new low following the incidents, with the United States and Europe hitting Moscow with waves of sanctions over the spy scandals and the conflict in Ukraine.
In his annual press conference this month, Putin said Western pressure was aimed at restraining a resurgent Russia.
"There is only one aim: to hold back Russia's development as a possible competitor," he said. "This is connected with the growth of Russia's power."