The Port Elizabeth Museum, which blends cultural with natural history, is the third oldest in South Africa and is the parent unit of Bayworld. The museum consists of a Dinosaur, Marine, Bird, Maritime History, Costume and Local History Halls, as well as a Curiosity Corner, Xhosa Beadwork Gallery andthe First People of the Bay exhibit. Other diverse temporary exhibits in the fields of natural science, archaeology and geology are also regularly on display in the Museum.

Particularly noteworthy exhibits are the 15m skeleton of the last Southern right whale harpooned in Nelson Mandela Bay; a life-sized reconstruction of the giant local prehistoric dinosaur known as Algoasaurus; a replica of the Dias Cross; and a 5m bronze cannon dated 1640, recovered from a Portuguese galleon wrecked near Port Elizabeth.