The phylogenetic relationships of members of the ciliate class Litostomatea were determined by a molecular phylogeny using the small subunit of the ribosomal RNA (ssu-rRNA) gene and a morphological phylogeny based on ultrastructural analyses of the group. Molecular analyses consistently supported the monophyly of Trichostomatia, Entodiniomorphida and the “Australian” trichostomes but provided limited support for a monophyletic Vestibuliferida and Haptoria. The results of the morphological analyses depended on the way in which the dataset was treated: “unordered” and “ordered” recovered a monophyletic Trichostomatia, Haptoria and the “Australian” trichostomes but challenged the monophyly of Entodinimorphida and Vestibuliferida; “dollo” recovered a monophyletic Trichostomatia and Entodiniomorphida but at the cost of a greatly longer tree than either “unordered” or “ordered” datasets. The monophyly of each “Australian” trichostome family was supported in all analyses and by both approaches. These results suggest that the trichostome ciliates may have become associated with mammals in Gondwana with the “Australian” trichostome ciliates entering Australia with primitive herbivorous marsupials. Subsequent diversification of the “Australian” families was probably a result of dietary specialization and oral and cortical synapomorphies define each family. We decline at this time to erect a formal taxon name for the “Australian” trichostomes due to the instability of other superfamilial taxa within the Litosomatea and concerns about the stability of tree topology until a better taxon sample of litostome ciliates is available.