The FSB, which said the American had been detained on December 28, said in a statement that a criminal case had been opened against him. It did not provide any detail about the nature of the alleged espionage, Reuters reported.
The US Embassy in Moscow could not immediately be reached for comment.
Russia's relations with the United States have soured since Moscow annexed the Crimean peninsula from Ukraine in 2014.
Since then the US and other Western countries have imposed a wide range of sanctions against Russian officials, companies and banks.