Michael Wenzel, 25, Robert Lee Benac, 28, and Spencer Heintz, 23, were all charged with two counts of aggravated animal cruelty each.
Florida Fish and Wildlife Conservation Commission officials were alerted to the video after sports fisherman and shark hunter Mark Quartiano, or "Mark the Shark", posted the video on his Instagram account when the footage was sent to him.
Quartiano told CNN he was "horrified" by the incident and that he posted the clip in the hope the men in the video would be identified.
"I've been shark fishing for 50 years and I've never seen a disrespect for an animal my entire career that was that evil," he said.
The clip was watched by thousands of people sparking outrage online.
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Florida wildlife officials began investigating after the video surfaced.
The video shows three men laughing and smiling as the animal visibly struggles in the boat's wake.
One man can be heard saying "the shark looks almost dead".
"As we've said since this video and other images came to light, these actions have no place in Florida, where we treasure and conserve our natural resources for everyone," Commission chairman Bo Rivard said.
"We appreciate the patience and support of the public as our law enforcement investigators worked with the Hillsborough County State Attorney’s Office to identify a number of serious violations that will be brought to the courts for adjudication.
"It is our hope these charges will send a clear message to others that this kind of behavior involving our fish and wildlife will not be tolerated."
After the investigation, Florida wildlife officials also charged two of the men, Wenzel and Benac, of misdemeanor count of illegal method of take for the shark.
A spokesperson for the Fish and Wildlife Conversation Commission told CNN investigators found that the men first shot the shark.
"Because they first shot the shark, it warranted two separate charges for animal cruelty," he said.
A third-degree animal cruelty charge carries a sentence of up to five years in prison and a fine of up to $10,000.
