The discovery was made at a small commercial business park where a company called Ram Striping leases warehouse space and keeps equipment.
Investigators said the paint on the tortoise, named Raphael, is the same paint they found around his burrow and the same paint that Ram Striping uses on pavement.
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Investigators believe Escalera disposed of the paint by dumping it in the hole.
Several days later, a couple driving on County Road 455 spotted the tortoise crossing the road and took it to an animal sanctuary for help.
Experts said the paint could have affected the tortoise in many ways, including disrupting his heat regulation and causing poisons to leach into his body, as well as destroying his natural camouflage protection.
Escalera, who said he didn't know the gopher tortoise was in the hole, was charged with littering and with injuring the endangered gopher tortoise.
Charges were filed through the state attorney's office, so an arrest was not immediately made. The company declined to comment.
Workers at the animal sanctuary were able to remove the paint from Raphael and nurse him back to good health. He was released back into the wild.
If convicted, Escalera faces up to $600 in fines and up to 60 days in jail.