The U.S. envoy to Russia accused the Moscow city court of basing its verdict on a secret and unproven trial.
The defendant Whelan showed a sign during the trial that read: "False Trial!" After learning of the conviction, he asked the President of the United States to intervene.
Whelan is charged with obtaining classified information from the Russian state, but it is not yet known what information the former Marine had access to.
#Russia court found ex-US marine Paul Whelan guilty of spying for the United States on Monday and sentenced him to 16 years in jail after a closed trial which US diplomats said was unfair and opaque. https://t.co/La6NY12YT6
U.S. Ambassador in Russia John Sullivan was present at the Moscow tribunal.
According to Sullivan, the court proceedings blatantly violated human rights and international legal standards.
U.S. Secretary of State Mike Pompeo demanded Whelan's immediate release.
"We are outraged by the Russian decision to convict American citizen Paul Whelan after a secret trial, with secret evidence, and without proper permission for defense witnesses," Pompeo said in a statement.
Whelan, 50, has been in Russian custody for the past year and a half.