There are two species groups within Australimyza, an Australian group (victoria species group) and a New Zealand group (australensis species group), plus one ungrouped species.

Although Harrison (1953) placed Australimyza in Milichiidae when he described the genus, he then recognized that it was atypical (absence of frontal setae, proboscis not elongate and geniculate) for this family. Harrison also noted that Australimyza was the sole representative of Milichiidae from New Zealand. His placement in Milichiidae was based on the presence of convergent, anterior orbital seta, the absence of anepisternal setae, and having the costa broken twice. Colless and McAlpine (1970, 1991) referred the genus to the family Carnidae where it was accorded subfamilial status in their later publication. Grimaldi (1997) followed this view and included Australimyza in his phylogenetic analysis of Carnidae. In contrast, Griffiths (1972) suggested in his study of acalyptrate phylogeny that Australimyza be accorded family (Australimyzidae) and prefamily (Australimyzoinea) status and be placed between his prefamilies Micropezoinea and Diopsinoinea. McAlpine (1989) concurred with recognizing Australimyzidae as a distinct family, but his phylogenetic placement of the family was near the Carnidae and Braulidae in the superfamily Carnoidea. Buck (2006) tentatively supported the monophyly of Carnoidea as a working hypothesis and placed Australimyzidae as the sister group of Inbiomyiidae and these together as the sister group of Carnidae. Support for the relationship between Australimyzidae+Inbiomyiidae and Carnidae, however, is not very strong (five or six pairs of pseudotracheae, subepandrial sclerite absent). Two new characters are presented in this paper. The first is the presence of a multichambered female ventral receptacle in Australimyzidae that has so far not been found in any other family of Carnoidea (the shape of the receptable in Inbiomyiidae needs elucidation) but has been observed in some families of Opomyzoidea (Kotrba and Baptista 2002), for example. The second new character set is the morphology of the larvae. Larvae, however, are not known for Inbiomyiidae, so that comparison cannot be made with this family. The larvae of Australimyza agree with larvae of Carnidae (Meoneura, Carnus) and Acartophthalmidae in having a weakly sclerotized cephaloskeleton (Engel 1930, Papp 1998, Papp & Ozerov 1998) but differ in other respects (presence of antennal papilla and tubercules, and general shape of anterior and posterior regions in Australimyza). The presence of tubercles on the thoracic body segments is also found in Braulidae, however, Braula does not have tubercles on the abdominal segments and the tubercles themselves are shaped differently. The shape of the posterior spiracle is similar to Milichiidae, Chloropidae and others, but in these families the spiracles are situated on protuberances. The morphology of the larvae has not been used previously in the phylogenetic analysis of Carnoidea or related superfamilies because knowledge about larvae is incomplete. Therefore it is difficult to evaluate the characters of Australimyza larvae. However, everal similarities between larvae of Australimyzidae and other families of Carnoidea could support placement of Australimyzidae in this superfamily. It is well possible that the relationships of Australimyza+Inbiomyia will change if larval characters and molecular data are taken into account. (Brake & Mathis 2007)

A molecular analysis by Winkler et al. (2010) found strong support for a close relationship between Australimyzidae and Xenasteidae (Inbiomyiidae were not studied), and evidence that these two families are not closely related to any "opomyzoid" families.