Khodorkovsky, 45, and Platon Lebedev, 42, are already serving eight-year sentences for tax evasion and theft charges. Many critics say the charges were politically motivated.
The new charges against them include the embezzlement of more than 890 billion rubles ($25 billion at the current rate of exchange) and laundering 487.4 billion rubles and $7.5 billion.
Preliminary hearings on the second criminal case against them are due to start on March 3.
Moscow City Court spokesperson Anna Usachyova said on Tuesday that Khodorkovsky and Lebedev had been transferred to detention centers in Moscow.
Once Russia's largest oil producer, Yukos collapsed after charges of tax evasion led to the company being broken up and sold off to meet debts. The bulk of the company's assets were bought up by state-run oil company Rosneft and it was declared bankrupt in 2006.
