Suspects Robby Stratton and Kevin Scott Keene are charged with illegal possession of an American alligator, illegal exhibition of dangerous wildlife and cruelty to animals, FWC spokesperson Karen Parker said in a statement.
The agency is still searching for other people that were seen in the video abusing the gator.
Both men could face a fine of $5,000, or up to five years in prison.
Disturbing images are emerging of men handling an alligator seen in a viral video of a man on a beer run with the reptile under his arm.
The additional video appears to show Robby Stratton and others passing the alligator around in the moments before he ran through a convenience store holding the reptile.
On Saturday, Stratton told Action News Jax he didn't know where the animal came from. In the new video, he appears to describe how his friend caught the animal.
"This (expletive) had a weed eater in his hand, looked over and found him," Stratton said in the video.
"I was working and he came up to me and I dove on his (expletive)," said the man as he described capturing the animal from the wild.
The video takes a disturbing turn when another man appears to step on the animal, then grab it by its neck and hold it in the air. He then shouts, "Florida State, baby! Florida State, baby! Florida State, baby!"
For the second time in less than 24 hours, Action News Jax ran into Robby Stratton as he bought beer at the same convenience store. He was asked why he was seen holding the alligator, and if he had any knowledge of where animal came from.
He said he's seen the new video, but had been drinking prior to this incident as well. He said he was under the impression the alligator was not real at the time. He told Action News Jax he released the animal into a creek near the convenience store after he realized it alive.
Stratton said he didn't run into the store looking for publicity.
“I know I didn’t go out and say, 'Hey man, let’s go viral tonight,'” Stratton said on Saturday night.
Stratton said he doesn’t remember anything from the night of the convenience store video, citing the influence of alcohol.
We asked Stratton twice if he regretted the incident and seemed to get conflicting responses. After first posing the question, a passerby began to voice her concerns.
"You should regret it," she told him. "The FWC is coming after you!"
"She regrets it," he said in response. "They already talked to me!"
We asked a second time later in the interview.
''I definitely regret it," Stratton said. "It was stupid, it was stupid.”
The FWC is presently investigating the video of Stratton running into the convenience store. He could face a fine of $5,000, or up to five years in prison.
FWC officials have not responded to questions about whether they are aware of the additional video.