Ellen Aguiar filed the court documents with the Broward County Circuit Court on Thursday to become the conservator or temporary guardian of Aguiar's estate, which is valued at more than $100 million.
On Wednesday morning, Aguiar's 31-foot fishing boat washed up on a Fort Lauderdale beach with the engine running and lights on, but with no sign of its Brazilian-born owner.
The U.S. Coast Guard and multiple police agencies launched a search for Aguiar, but the Coast Guard search suspended their search on Thursday night.
The suspension of the search, Aguiar's mother's legal filing and the lack of a body have raised questions about what exactly happened on Aguiar's boat after he left his dock on Tuesday night.
Fort Lauderdale Det. Travis Mandell said that surveillance footage shows Aguiar getting on his boat alone and setting sail alone.
"There's no evidence at this point to suggest that anyone else was on the vessel except Guma," Mandell said.
As for what happened when he made it out to sea, "Anything is possible," Mandell said.
Ellen Aguiar said on Thursday morning that she wanted to hope for the best, but was realistic about the fate her son may have met since it appeared that his boat was caught in a storm.
"I would be delighted to hear that he was kidnapped and being taken great care of, and I believe in miracles and would hope for a miracle. I think, realistically, what happened is pretty clear," she told ABCNews.com. "The likelihood is that he was tossed off the boat into the waves. The boat was found, but the body has not been found."
Later on Thursday she filed court documents for control of his estate, which includes $65 million in bank assets, $35 million in Israeli real estate, the $5 million Florida home he shares with his family, and seven cars and a yacht valued at over $3 million.
"The Absentee disappeared as the result of mental derangement, or other mental cause, or, in the alternative, disappeared under circumstances indicating that he may have died, either naturally, accidentally, or at the hand of another," the document states.
Guma Aguiar's cell phone and wallet were found on his boat when it ran aground, according to the filing.
Aguiar, 35, made his fortune in 2006 when he and his uncle Thomas Kaplan sold their Texas-based energy company for a reported $2.5 billion. The two have been in a messy legal battle since 2009 over the division of the money.
They went on to say that his was the victim of what amounted to "psychological terrorism."