The Natural History Museum Basel's amphibian and reptile collection comprises more than 32,000 objects of almost 2500 reptile species and more than 900 amphibian species. The majority of these come from the South East Asia.

The objects in the herpetological collection date primarily from the middle of the 19th and start of the 20th centuries. The beginning reach back to the university collection from the middle of the 19th century. At the start of the 20th century, the collection was expanded with objects from Indonesia. The material from Bhutan dates from the 1970s.

The collection also includes extinct species such as the Quito stubfoot toad Atelopus ignescens or the Cape Verde giant skink Macroscincus cocteaui. This can only be found in few other collections around the world.

Around a quarter of the objects in the collection come from Europe, while the rest come from worldwide locations and in particular the Indonesian region.

Jean Roux provides a historic insight into the beginnings of the collection in the work published in 1924 entitled 'Notice historique sur la collection erpétologique du Museum d'Histoire naturelle de Bâle', which appeared in the journal entitled 'Verhandlungen der Naturforschenden Gesellschaft Basel'.