The heart of the Hefner Museum is the Main Gallery, 100 Upham Hall. It features an engaging array of permanent and rotating exhibits and displays, and showcases many of the Hefner's most beloved specimens, including a great Kodiak bear, a passenger pigeon, mammoth bones, and a manatee.

The Paul Daniel Classroom (106 Upham Hall) is a primary gathering place at the Center and is used for group inquiries, hands-on activities, and workshops. Exhibits around the room highlight the diversity within animal groups: coral, sponges, insects, fish, amphibians, reptiles, and birds.

Adjoining the Main Gallery, Hoofs, Horns, Antlers, and Claws highlights the amazing biodiversity of ungulates (hoofed animals) from around the world. An endowment from Richard E. and Dorothy Francis made possible this exhibit, which features an extensive collection of hoofed animal mounts and a large Kodiak bear.

Designed with young children in mind, the Imaginarium (112 Upham Hall) is an interactive space where children explore and learn about animals and habitats. The large ecosystem murals and magnetic animal pictures, animal costumes, larger-than-life bird nest, model decomposing log, and beehive all invite children to play and discover.

Opened in 2011, the Mollusc Gallery houses more than 25,000 specimens from marine, freshwater, and terrestrial habitats. The exhibits in this beautiful pearl of a space was largely designed by Miami undergraduates in a professional writing class taught by Dr. Jean Lutz of the Department of English.