A Manhattan judge has declined to dismiss fraud and breach of fiduciary duty allegations against John Thain, the chief executive officer of the New York Stock Exchange, by a former seatholder of the exchange.

But the judge, Justice Charles E. Ramos, dismissed breach of fiduciary duty and negligent misrepresentation claims against the exchange itself in connection with its 2005 merger with Archipelago Holdings and its transformation from a not-for-profit to a public company.