The name comes from the word scrotum, a pouch in which the testes permanently reside in the adult male. All members of the group have a postpenile scrotum, often prominently displayed, except for some aquatic forms and pangolin (which has the testes just below the skin). It appears to be an ancestral character for this group, yet other orders generally lack this as an ancestral feature, with the probable exception of Primates.
The clade Scrotifera is based on evidence from molecular phylogenetics. The monophylogeny of the group is well supported, but there is some debate about the internal order, with Pegasoferae being an alternative to that shown in the following cladogram.