The move was widely expected, coming days after the casino operator's namesake tycoon, Chairman and founder Donald Trump, walked away from the company.
The casino operator had assets of about $2.1 billion and total debts of about $1.74 billion on December 31, 2008, it said in its filing with the U.S. Bankruptcy Court for the District of New Jersey.
The company missed a $53.1 million bond interest payment due on December 1 as a sharp downturn in consumer spending hit casino revenues, prompting bondholders to push for bankruptcy.
Trump, the most flamboyant player in an industry filled with colorful, headstrong executives, said the company represents less than 1 percent of his net worth, and that my investment in it is worthless to me now.
No stranger to bankruptcy, Trump Entertainment Resort Holdings went into chapter 11 in 2004, from which it emerged a year later with Trump having relinquished the position of CEO.
Friday's statement did not say when Trump's resignation would be offered or take effect. His daughter Ivanka Trump is also resigning, it said.
Nine affiliates of the casino operator including Trump Plaza Associates, Trump Plaza Associates, Trump Marina Associates and Trump Taj Mahal Associates simultaneously sought protection, according to the filing.
(Reporting by Christopher Kaufman in New York and Ajay Kamalakaran in Bangalore, editing by Dave Zimmerman)