The club has been in default on its obligations to Trump for months due to the company's financial constraints and a difficult business climate in Puerto Rico, Eric Trump said.
The golf resort, which has hosted the Puerto Rico Open tournament, filed for bankruptcy protection as Coco Beach Golf & Country Club. It also filed a motion to sell its assets, according to the property's attorney Charles Cuprill. He said the company has at least one interested buyer.
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In a phone interview Monday, Cuprill said Coco Beach has experienced operational losses for the past two years.
"The critical economic crisis in which Puerto Rico is going through has affected all sectors of the economy," including the entertainment industry, Cuprill said.
Coco Beach listed assets of $9.23 million and liabilities of $78.07 million according to the filing with the Puerto Rico bankruptcy court.
In 2014, Trump Entertainment Resorts, a Trump-branded casino in Atlantic City, filed for bankruptcy protection due to declining revenue and increased competition.
—CNBC's Ryan Ruggiero contributed to this report.