The company has given no reason for Thain's departure, but it follows news that Merrill Lynch had moved up its year-end bonuses, doling out cash just days before it was officially acquired by Bank of America on Jan. 1.
A company spokesman issued a short statement: "Ken Lewis flew to New York today to talk to John Thain. And it was mutually agreed that his situation was not working out and he would resign."
Thain was heading a wealth management division of the two firms' merged businesses. He went to Merrill Lynch after leading the New York Stock Exchange and before that, serving as chief operating officer at Goldman Sachs.
Merrill, which reported a $15.45 billion fourth-quarter loss, was acquired by Bank of America in a government-brokered deal the same day the Lehman Brothers Holdings Inc. collapsed.