Whelan and his family have always denied he is a spy and have accused Russia of fabricating the case against him in order to use him as a bargaining chip in its relations with the United States.
In court on Monday, Whelan denounced the trial as a "sham" and part of a pre-planned operation by the Russian security services.
"We have proven my innocence," Whelan told reporters while standing in a glass cage in the court room, flanked by men in masks. "We have proven fabrication. This is slimy, greasy corrupt Russian politics, nothing more, nothing less."
"The treatment of Paul Whelan at the hands of Russian authorities has been appalling. Russia failed to provide Mr. Whelan with a fair hearing before an independent and impartial tribunal," the statement read. "We demand Paul Whelan's immediate release."
The U.S. ambassador to Russia, John Sullivan, outside the court told reporters the judge had provided no evidence to justify Whelan's detention.
"I've described these proceedings as a mockery of justice and today just confirmed it," Sullivan said. "An American citizen has been sentenced to a term of 16 years for a crime for which we have not seen evidence."
Whelan's case is classified secret and Russia's authorities have never publicly provided details of the charges against him. The trial have been held almost entirely behind closed doors and it has been rushed through since it began in April.
His defense has said he is the victim of a crude frame-up by the FSB, which they said used a long-time friend of Whelan's to set him up.
According to his lawyers, the Russian friend, who was an FSB officer, planted classified materials on Whelan while visiting his hotel room in December 2018. Whelan had thought the friend was bringing him a memory card containing photographs of a trip to a monastery town they had taken together in spring earlier that year. Instead, unknown to Whelan, the card held the classified materials, according to his defense.
A few minutes later, FSB officers burst in and detained Whelan.
Whelan's lawyers have not named the friend because of secrecy rules, saying only that he is a member of Russia's security services. But Whelan's family have identified him as Ilya Yatsenko. The Russian newspaper, Kommersant has reported that Yatsenko is a major in the FSB's Department 'K', the powerful division handling economic crimes.
Since the moment of his arrest, there has been speculation that Russia would seek to trade Whelan in a possible exchange for Russians imprisoned in the United States.
After the hearing, Whelan's Russian lawyers said that the FSB had made clear to them that Russia now intended to seek to swap Whelan.
"I understand that that question is already decided higher up," Vladimir Zherebenkov, Whelan's lawyer told reporters.
Zherebenkov said that the FSB had suggested to him that it did not make sense to appeal Whelan's verdict since it would slow down any attempt to trade him.
"There is a suggestion and thought from some agents of the security services, 'Guys, why do that, when the question of exchange will be solved quicker?'" Zherebenkov said.
Zherebenkov said he believed Russia wants to trade Whelan for two Russians currently serving long jail sentences in the U.S., Konstantin Yaroshenko, a pilot convicted of drug smuggling, and Viktor Bout, a notorious arms dealer suspected of links to Russian intelligence.
Russian officials have previously noted Whelan can be traded if pardoned by President Vladimir Putin, which can only occur after a conviction. Zherebenkov said they had intended to appeal Monday's verdict but that they would first discuss it with Whelan.
Shortly after the lawyer's comments, Viktor Bout's wife Alla Bout told the Russian state news agency RIA Novosti that she was ready to write an appeal to the U.S. government asking for Whelan to be exchanged for her husband. She said that she had already discussed the possibility of such a trade with the Russian ambassador to the U.S. during a meeting last September.
Russian officials and state media have for years campaigned for Bout and Yaroshenko's release, painting them as unjustly imprisoned. Bout, was accused by U.S. prosecutors of running an international arms trafficking network, was sentenced to 25 years jail in 2011 after he was arrested in Thailand in a Drug Enforcement Agency sting operation.
Bout, who has been nicknamed the "Merchant of Death" and whose life was the basis for the protagonist in the Nicholas Cage film, "Lord of War," was convicted of conspiring to sell arms to a Colombian terrorist group. Yaroshenko is serving a 20 year sentence on a conviction for conspiring to smuggle cocaine into the U.S.
Asked about a possible exchange, Ambassador Sullivan said he couldn't comment on a possible exchange.
"I'm not authorized to discuss exchanges. Now, when Paul has been convicted, I'm seeking justice for Paul. We are seeking not an exchange, but justice for him" Sullivan told reporters at the court.
Whelan's family have said they believe Russia took Whelan prisoner in order to seek a trade for Bout, Yaroshenko, as well as other possible concessions from the U.S., such as the return of diplomatic properties seized in retaliation for Russia's meddling in the 2016 election.
Immediately after the verdict, they released a statement denouncing it and appealing to the U.S. government to take "immediate steps" to bring Whelan home.
"The court's decision merely completes the final piece of this broken judicial process. We had hoped that the court might show some independence but, in the end, Russian judges are political, not legal, entities," the statement released by Whelan's brother David said. "We look to the U.S. government to immediately take steps to bring Paul home."
But David Whelan said the family did not now intend to ask the U.S. government to seek a prisoner exchange and expressed doubts about how possible it would be. It is unclear how willing the U.S. will be to exchange Russians convicted of serious crimes for Whelan, who it considers to be entirely innocent.
"Prisoner exchanges in hostage diplomacy only encourage the bad actor state to take more hostages," David Whelan told ABC News in an email. "Paul is a tourist, not a spy," he said, noting that a number of the trades, including Bout and Yaroshenko, that Russia has suggested it wants are not equivalent. "I would completely understand if the U.S. was reluctant to engage in a swap. I could completely understand how the U.S. would prefer punitive measures instead, like sanctions, rather than creating a reward for coercive detentions," he said.
"If the U.S. government decides that a trade of some sort is appropriate, I wouldn't argue against it. But I would not argue for it as the only way to secure Paul's freedom," David Whelan said.
Whelan's family said they would look to President Donald Trump to help release him and said they were relying on David Urban, a Washington, D.C.-based lobbyist and adviser to Trump's election campaign, to speak to the White House.
The Kremlin's spokesman Dmitry Peskov, responding to questions after the hearing, denied that Whelan was a "political hostage." He declined to comment on the possibility of a trade, telling reporters in a daily briefing call that the Kremlin is not involved in Whelan's case.
Former U.S. intelligence officials have also said Whelan's case has the hallmarks of a KGB-style frame up, similar to those seen in the Cold War. They have said Whelan's background would have made him an unlikely choice for an American intelligence operative.
In addition to the U.S., Whelan also holds British, Irish and Canadian citizenship. He left the Marines after he was convicted in a court-martial on larceny charges in 2008 and received a bad conduct discharge. Whelan was a global security director for the autoparts supplier BorgWarner when he was arrested in Moscow.
A self-described Russophile, Whelan has traveled many times to Russia as a tourist and traveled in the country with friends, according to his family.
In court on Monday, Whelan held up a sign with the words "Sham Trial!" and "Meatball surgery" written on it, a reference he said to an emergency hernia operation he was given in June after being denied treatment for months.
He told journalists his detention was part of a pre-planned operation and that the Russian ambassador to the U.S., Anatoly Antonov had been aware of it before his trip to Moscow when he was arrested.
"It's absolutely ridiculous," Whelan said. "They say I'm a brigadier general. I'm not."
Tanya Stukalova provided reporting from Moscow.