The body of Mr Laundrie, who had been missing for over a month, was identified using dental records.
Mr Laundrie, who was a person of interest in Gabby Petito's death, returned to Florida last month from a joint road trip without his partner.
Her body was later found in Wyoming, where the couple had been travelling.
"On October 21, 2021, a comparison of dental records confirmed that the human remains found at the T Mabry Carlton Jr Memorial Reserve and Myakkahatchee Creed Environmental Park are those of Brian Laundrie," the FBI said in a statement on Thursday.
A lawyer representing Mr Laundrie's parents released a statement, saying: "Chris and Roberta Laundrie have been informed that the remains found yesterday in the reserve are indeed Brian's.
"We have no further comment at this time and we ask that you respect the Laundries' privacy at this time."
On Wednesday, officials said that the remains had been discovered in a part of the park that until recently had been underwater. Other items, including a backpack and notebook belonging to Brian, were also found during the search.
According to NBC News, bones and a skull were discovered during the search.
In a short news conference on Thursday, Lee County Sheriff Carmine Marceno praised officials for working under "treacherous conditions" in the park.
He described the chest-deep water as being filled with rattlesnakes and alligators.
"It's not like you're searching a house or a car. These areas are huge and they are covered by water," he told reporters gathered outside the closed park.
Who is Brian Laundrie?The case of Ms Petito, 22, and Mr Laundrie, 23, sparked nationwide media attention.
The couple had spent their summer on a road trip through national parks, documenting their nomadic "van life" trip on social media.
Ms Petito's parents reported her missing on 11 September after they were unable to contact her since the end of August.
It eventually emerged that Mr Laundrie had returned to Florida without Ms Petito on 1 September. Her family repeatedly appealed for her fiancé and his family to co-operate with investigators, but he then went missing himself.
His parents told police they last saw him on 13 September - when he went hiking alone and never returned.
The parents, who have been condemned by the Petito family for not doing more to aid investigators, joined the search party on Wednesday. Chris Laundrie, the father, was the person who discovered a bag belonging to his son, the family lawyer told US media.
The rapid discovery of Mr Laundrie's remains and other evidence following the participation of his parents in the search has led some to speculate that they may have planted his remains or evidence.
However, Steve Bertolino, the couple's attorney, told CNN that any suspicion that his clients planted evidence at the scene was "hogwash".
He added that Chris Laundrie had made a chance discovery.
Ms Petito's body was eventually discovered in Wyoming on 19 September. A coroner ruled last week that she had been strangled to death and left for weeks before her body was found.
Mr Laundrie was not charged with crimes relating to Ms Petito's killing. However, the FBI issued a federal arrest warrant and charged him with fraudulently using her debit card after her death.