Judge Viktor Danilkin sentenced Khodorkovsky to 14 years after convicting him of stealing oil from his own company and laundering the proceeds.
The 14-year sentence, which was what prosecutors had demanded, will be counted from his 2003 arrest and include a previous term in prison. Khodorkovsky is in the final year of an eight-year prison sentence.
Putin, now prime minister, is seen as the driving force behind the unrelenting legal attack on Khodorkovsky, who challenged him early in his presidency.
As he considers a return to the presidency in 2012, Putin appears unwilling to risk the possibility that a freed Khodorkovsky could help lead his political foes.
The outcome of the second trial exposes how little has changed under President Dmitry Medvedev despite his promises to strengthen the rule of law and make courts an independent branch of government.
"It's a very cruel and absurd sentence that proves the well-known fact that Russia has no independent courts," said Lyudmila Alexeyeva, a veteran rights activist and chairwoman of the Moscow Helsinki Group. "An independent court would have acquitted the defendants and punished the investigators who concocted the charges."
Following a 20-month trial in Moscow, the judge convicted Khodorkovsky and his business partner Platon Lebedev on charges of stealing almost 30 billion dollars (£20 billion) worth of the oil that his Yukos company produced from 1998 to 2003 and laundering the proceeds. Lebedev also was sentenced to 14 years.
Defence lawyers said much of the judge's verdict was copied from the indictment and the prosecutors' final arguments.
The defence called the charges ridiculous, saying they reflected a lack of understanding of the oil business, including the payment of transit fees and export duties. Numerous witnesses, including current and former government officials, testified that Khodorkovsky could not have stolen what amounted to almost all of the oil Yukos had produced.
The charges also contradicted the first trial, in which Khodorkovsky was convicted of evading taxes on Yukos profits.
Danilkin's conduct during the trial had raised some hopes among Khodorkovsky's family and supporters that he would prove to be more independent than the judge in the previous trial, who openly supported the prosecutors. Those hopes were dashed as soon as Danilkin began to read the verdict.
"They must have tortured him to get him to say what he did," said Khodorkovsky's mother, Marina. "He has put his title of judge in shame."
Khodorkovsky had angered Putin by funding opposition parties in parliament, which at the time had the power to oppose Kremlin policies and influence the choice of prime minister. He also pursued his own oil export plans independent of the state pipeline system, and publicly questioned the appearance of Kremlin corruption.
"The court decision has nothing to do with the law or justice," said Boris Nemtsov, a former deputy prime minister who is now among the leaders of the opposition. "It's Putin's personal vendetta."
The guilty verdict was widely condemned in the West as being driven by politics rather than the rule of law. The criticism, however, only angered Russia's government, which pointedly told the US and Europe to mind their own business.
The defence lawyers said they planned to appeal, a process that could take months, and in the meantime Khodorkovsky and Lebedev will remain in a Moscow jail.
After the first trial, Khodorkovsky was sent to a labour colony in eastern Siberia near the Chinese border, while Lebedev served the first part of his sentence in a prison above the Arctic Circle.
"You cannot count on the courts to protect you from government officials in Russia," Khodorkovsky said in a statement read outside the courthouse by his lead lawyer.
In the statement, read by Vadim Klyuvgant to reporters outside the courthouse, Khodorkovsky expressed some optimism, saying: "But we have not lost hope and nor should our friends."
Khodorkovsky also said the verdict showed that the "Churov rule" was alive and well, referring to a comment made a few years ago by Vladimir Churov, the chairman of the Central Election Commission, that his first rule was that Putin is always right. And if he's not, "it means I have misunderstood something".
"The judge was only the nominal author of the verdict," Klyuvgant said.
When the sentence was announced in the courtroom, Khodorkovsky's mother burst out with an emotional "curse you and your children," seemingly directed at the judge.
Speaking outside the courthouse before the television cameras, Marina Khodorkovskaya addressed her remarks to President Medvedev. "Mr President, a man of the same generation as my son, aren't you ashamed to be the servant of a conscienceless, immoral man," she said.
Criticism of the trial quickly began to pour in from across Europe.
"I am disappointed by the verdict against Mikhail Khodorkovsky and the harsh sentence," German Chancellor Angela Merkel said in a statement.
"The impression remains that political motives played a role in these proceedings. This contradicts the intention repeatedly voiced by Russia of pursuing the road to the full rule of law."
The president of the European Parliament in Brussels said the longer prison sentence for Khodorkovsky showed that Russia still had a long way to go in its promised reform of the judiciary.
"The trials of Mikhail Khodorkovsky were the litmus test of how the rule of law and human rights are treated in today's Russia," Jerzy Buzek said in a statement. "In effect it has become the emblematic symbol of all the systemic problems within the judiciary."
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