The 22-year-old man driving the pickup said that he and his female passenger were coming from an underpass where they were trying to collect frogs and snakes.
The driver showed the deputy a bag near his feet with clothes and personal items in it. However, the reptiles were regulated animals and citations were written for both Clemons and Machan-Le Quire.
The woman also had 41 three-stripe turtles in a backpack, deputies say.
Asked by the officer, "Do you have anything else?" the woman replied by reaching into her pants and withdrawing a baby alligator. Then she pulled the alligator from her trousers.More news: Los Angeles Lakers' LeBron James stunned by Magic Johnson's 'weird' exit
NBC Miami called the incident an "only in Florida" moment.
He gave the deputy permission to search bags in the truck.
Deputies said the Florida Fish and Wildlife Conservation Commission then came and took over the investigation.
A spokesperson for the state agency did not immediately respond to ABC News' request for comment Tuesday morning.