The alligators were found in a South Daytona backyard after a woman pulling weeds discovered the beasts, police said.
The gators, 12 and 14 years old, were located Thursday night after a neighbour was pulling weeds and heard a knocking sound on a fence, South Daytona police said.
They said the woman saw one of the gators slapping the fence with its tail.
The woman and her husband had another neighbour call police and officers spotted two gators in the fenced-in yard, the WKMG-TV reported.
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"It's running around because this person was cutting the grass and pulling out weeds and then all the sudden they heard a (noise) and hit it hard and they looked and they saw it," the caller said.
Photos taken from a neighbour's yard showed the gators in a long makeshift pen with two small pools of water.
South Daytona police said the homeowner is on a vacation in Kentucky and told officials that he had raised the animals "from the egg."
South Daytona city does not permit alligators to be kept within city limits, and the owner, who does not have a license to keep the animals, could face a misdemeanour charge, police said.
FWC investigator Rick Brown said the gators appeared to be healthy and well-fed.