The 19-year-old is accused in a string of crimes across the U.S. The Washington state native is suspected of stealing cars, boats and at least five airplanes.
Harris-Moore was on the plane with Bahamian authorities as well as FBI agents, but he did not know FBI agents were aboard, said John Gillies, FBI special agent in charge of the Miami office. The FBI did not have any authority to arrest Harris-Moore in the Bahamas and waited until he reached Miami to take him into custody, Gillies said.
Earlier Tuesday, Harris-Moore pleaded guilty in the Bahamas to illegally entering the country. He had been arrested in the island country Sunday following a high-speed boat chase.
The charge stemming from his alleged crash of a stolen plane on Great Abaco Island carried a $300 fine. His lawyer, Monique Gomez, said the U.S. Embassy would pay it. Gomez said Harris-Moore wanted to go home.
Authorities dubbed him the "Barefoot Bandit" because he allegedly committed many of the crimes without his shoes on.
It's likely Colton Harris-Moore will eventually be taken to Seattle, where he was indicted.
His mother, Pam Kohler, seemed relieved.
"I'm really tired," Kohler said from her home on Camano Island, Wash. "Yes, I look forward to seeing him."
Asked what she planned to say to her son when she saw him, she said angrily, "What kind of question is that?" and hung up the phone.
The Associated Press contributed to this story.