Mr Thain, who was named chief executive of Merrill 13 months ago following the ousting of Stan O'Neal, left BofA after a brief meeting with its chief executive, Ken Lewis, who is under pressure from shareholders for paying a premium for Merrill.
Since the deal was announced on September 15, Merrill has disclosed operating losses of $41.2bn for 2008, and BofA's share price has dropped about 80 per cent.
According to a person familiar with the matter, Mr Lewis believes Mr Thain had lost the confidence of many of the combined firm's employees and shareholders. Mr Thain was not available for comment.
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