At the end of a railway that passed through neighboring Anastasia Island, this park opened its doors in 1893 on St. Augustine Beach as a little tourist destination. Initially, the alligators were added to encourage tourists to visit the museum and purchase trinkets. However, the reptiles themselves quickly rose to the top of the attraction list.

The park relocated to its current position in the early 1920s as it gained popularity. After a terrible fire, the park's proprietors, who took over in the 1930s, began to rebuild and expand the facilities. In 1993, the park became the first location in the world to display every crocodilian species. This was done in honor of their 100th anniversary.

The zoo constructed a new Komodo dragon exhibit in 2008 and a display of lizards and snakes native to Southeast Asia.