The board voted at an extraordinary shareholders meeting over the weekend to replace him with Andrei Melnichenko, founder and head of MDM, the bank said in a statement. Vladimir Rykunov, Melnichenko's deputy, was appointed chairman.
MDM did not reveal any details or reasons for the reshuffle.
Mamut -- a reputed Kremlin insider -- joined MDM in the fall of 1999 and is believed to have used his political connections to make it one of Russia's top banks.
Before joining MDM, he was a senior manager at Sobinbank, and was earlier a manager at KOPF bank, effectively defunct since the 1998 crisis.
Mamut's departure is believed to be linked to his dispute with the Central Bank over banking reform, said sources familiar with the situation.
Mamut -- on behalf of the Russian Union of Industrialists and Entrepreneurs, or RSPP -- had proposed a plan for sector reform that would dramatically cut the number of banks. However, the Central Bank fought the plan and won.
MDM management wanted to dissociate itself from Mamut, who they believed pushed his own political agenda despite the possibility of hurting MDM, said a source who declined to be identified.
"This [banking-reform dispute] may have easily been the last straw," said Richard Hainsworth, head of RusRating, a bank-rating agency.
An analyst with the Rating Information Center, however, said the reason for Mamut's departure was slightly different.
As MDM's chief and majority shareholder, Melnichenko was disappointed with Mamut's failure to push through the reform plan, which could have helped MDM boost its position in the regions, he said.
Hainsworth took a milder approach, saying Mamut's exit was a "parting of ways between Mamut and Melnichenko because of mutually inconsistent agendas."
MDM may lose out if Mamut's dismissal severs ties he helped establish with major companies, such as Sibneft, one analyst said.
Having finished at the bank, Mamut may be able to pursue a career in politics. The RBC news agency reported that he may be looking to become head of the RSPP.
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