The Musée d'Histoire Naturelle, in a former Jesuit college on Boulevard Amiral Courbet, has an unusually broad collection: prehistory, ethnography, zoology, geology. The prehistoric section, drawing on the rich finds from caves in the Languedoc and Cévennes, is particularly strong.
It's a small, atmospheric museum of the kind that has fallen out of fashion. The chapel of the former Jesuit college is occasionally used for temporary exhibitions and is worth seeing in its own right.