The Australian cephalochordate fauna consists of two genera and eight species. There are two endemic temperate-water species, Epigonichthys australis and E. bassanus, and six tropical species. Two of the latter, Branchiostoma minucauda and B. moretonensis, are endemic. The remaining four species, B. belcheri, E. cultellus, E. maldivensis and E. lucayanum, are found throughout the Indo-West Pacific Region. This study is based on the morphological study of 10 characters in 200 specimens. New synonymies are given for E. cultellus and the B. belcheri species-complex. The generic names Amphipleurichthys, Bathyamphioxus, Merscalpellus, Notasymmetron and Zeamphioxus are placed in the synonomy of Epigonichthys and the use of the junior synonym, Asymmetron, in place of Epigonichthys, is not supported. Information is presented on the distribution and habitat preferences of each species in Australia together with a key to the species likely to be found in Australia.