The biogeographic and phylogenetic relationships of six of the eight Australian genera of freshwater shrimp from the family Atyidae were investigated using mitochondrial 16S rDNA and cytochrome oxidase I sequences. Previous studies on two of the epigean genera (Caridina, Paratya) indicate that Australian species have strong links to congenerics from outside, with Australian members of Paratya being monophyletic and Caridina polyphyletic. The present study found that the endemic Australian epigean genus Australatya forms a strong clade with Pacific ‘Atya-like’ genera (Atyoida, Atyopsis), and that the endemic Australian epigean genus Caridinides falls within a clade containing Caridina species from the Australian ‘indistincta’ group. The two hypogean genera included in this study (Parisia, Pycnisia) form a strong clade in all analyses, implying an Australian subterranean speciation. The possibility of a relationship between Parisia/Pycnisia and an Australian Caridina species may have implications for the monophyly of the highly disjunct genus Parisia (Australia, Madagascar, Philippines). Parisia may descend from local Caridina species and represent convergent morphologies.