The vessel, the T.T. Zion, was discovered early Wednesday on the sand near East Las Olas Boulevard, the South Florida Sun Sentinel reported.
The boat's twin outboard engines were running and the boat's lights were on, but the multimillionaire owner, Brazilian-born businessman Guma Aguiar, 35, was nowhere to be found.
Rabbi Moshe Meir Lipszyc of Chabad Lubavitch of Fort Lauderdale said Aguiar's family is "completely devastated."
"They are all very, very worried about him," Lipszyc said. "We are hoping and praying for a miracle. We are hoping if he fell off the boat, that he was able to swim to shore. He is massively special and with God's help and all our prayers, we hope he will be OK."
Sea Tow Captain John See inspected the vessel and said there was no sign of blood, bait or fishing gear aboard the T.T. Zion, but that the tie bar connecting its outboard engines was broken.
If the tie bar was broken and the engines became unattached, "The second engine could turn sharply and pitch a boater overboard, or it could be difficult for its captain to steer," See said.
Fort Lauderdale Police searched the beach on ATVs, but said it was strange that Aguiar would go boating at night.
"It's extremely odd that Mr. Aguiar would venture out in such tumultuous seas and rip currents and impending bad weather conditions that were unfavorable for boating, even for the most seasoned captain," said Detective Travis Mandell.
"Our hope is that we will find Mr. Aguiar safe and sound," Mandell said. "Until then, we will continue with our searches and investigation."
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