The Brachycera is certainly a monophyletic group, with a large number of undisputed autapomorphies. The phylogeny of the lower Brachycera has been scrutinized intensively over the past 15 years. A recent quantitative reanalysis of morphological characters used to define relationships between the lower Brachyceran families attempted to summarize and synthesize this research (Yeates, 2002). This study revealed weak evidence for the monophyly of a clade containing Xylophagomorpha, Stratiomyomorpha and Tabanomorpha, and weak evidence for a monophyletic Asiloidea, and these findings are reflected in the supertree. The most basal lineage of Brachycera in the supertree analysis contains, Stratiomyomorpha plus (Xylophagomorpha + Tabanomorpha), reflecting the results of recent quantitative cladistic analyses. The infraorder Muscomorpha contains all brachyceran families except those belonging to Stratiomyomorpha, Xylophagomorpha and Tabanomorpha, and is a well-supported clade found on the supertree. The Nemestrinoidea, Asiloidea and Empidoidea are monophyletic, arising from the main stem of the Brachycera in that sequence. Evidence for the monophyly of nemestrinoids and asiloids is not strong, and they appear paraphyletic in some analyses. A number of asiloid families have received critical phylogenetic scrutiny in recent years, partly because of their proximity to Eremoneura.
Eremoneura is the muscomorphan lineage containing Empidoidea + Cyclorrhapha, and is one of the best-supported higher-level brachyceran clades with many synapomorphies. Recent morphological work has emphasised male genitalic characters for phylogenetic reconstruction in Eremoneura, however some analyses of molecular data are beginning to appear. There is strong evidence for the monophyly of the Empidoidea, and the Atelestidae, Hybotidae, Empididae and Microphoridae + Dolichopodidae from both morphological and molecular data.
Cyclorrhaphan monophyly is well supported by characters such as the invagination of the larval head capsule and modifications of the larval mouthparts, as well as pupation within the skin of the last larval instar. These are the most recognizable features of this landmark in dipteran evolution. Over the last 40 years only three workers have attempted to synthesize phylogenetic evidence on cyclorrhaphan relationships in a comprehensive fashion. All studies were not based on explicit data sets and results differed in many regards (Hennig, 1973; Griffiths, 1972; McAlpine, 1989). Exploration of new character systems applied broadly across cyclorrhaphan groups, for example from egg and larval morphology, female genitalia and internal morphology, and nucleotide sequences are urgently needed. There are a number of competing hypotheses regarding the relationships of the families belonging to the Lower Cyclorrhaphan grade, but the Syrphoidea are generally regarded the sister group to the Schizophora.