Khodorkovsky, 47, who was once the richest man in Russia, is thought by many to have been unfairly targeted by Putin, who wanted to thwart his political ambitions and influence. Khodorkovsky often financed opposition parties and expressed some interest in running for office.
He is already serving an eight-year prison sentence in Siberia after being convicted of tax evasion in 2005.
He was convicted today with his co-defendant Platon Lebedev on charges of fraud and money laundering involving Yukos, the now bankrupt oil company founded by Khodorkovsky. They will be sentenced either this week or after Jan. 10, at the end of the Russian New Year holidays. Khodorkovsky could face up to six to 14 more years in prison.
"The trial was a charade of justice, the charges were absolutely false, but I fear the sentencing will be very real," Vadim Klyuvgant, the lead defense lawyer, told Reuters in an e-mail.
Klyuvgant and the defense team plan to appeal the decision, which they claim was the result of the Kremlin's plan to destroy Khodorkovsky and his company.
The press was ordered out of the Moscow courtroom after Judge Viktor Danilkin read the verdict, preventing reporters from hearing him read out the details of the lengthy ruling, The Associated Press reported.
No explanation was given for the dismissal of the media.
Khodorkovsky, who once symbolized the ultimate oligarch, has been transformed into something of a famed political prisoner, with Amnesty International calling on Russian courts to overturn his conviction.
Germany's human rights commissioner, Markus Loening, called today's verdict an "example of arbitrary political justice."
Earlier this month, Putin compared Khodorkovsky to Bernard Madoff, who is serving 150 years in a U.S. prison for a massive Ponzi scheme that defrauded thousands of investors, and said "a thief should be in prison." Putin previously compared him to Al Capone.
Just hours before the verdict was announced, The Independent published an article saying that if Khodorkovsky was found innocent, it would mean that Russian President Dimitry Medvedev had finally become "his own man."
"A guilty verdict would prove that President Medvedev, who came to the power promising to end 'legal nihilism,' has not been able to step out of Mr. Putin's shadow," The Independent said.
"I will not be exaggerating if I say that millions of eyes throughout Russia and the world are watching this trial," he wrote.
"They are watching with the hope that Russia will still become a country of freedom and law, where the law is above the bureaucrat," he continued. "Where supporting opposition parties is not a cause for reprisals. Where special services protect the people and the law, and not the bureaucracy from the people and the law. Where human rights no longer depend on the mood of the czar, good or evil."