A phylogeny of the Chironomidae subfamily Podonominae, significant in the history of phylogenetic biogeography, is estimated from an analysis of four genes. Fragments of two ribosomal genes (18S and 28S), one nuclear protein-coding gene (CAD), and one mitochondrial protein-coding gene (COI) were sequenced from specimens representing 13 of 15 genera, and analysed using mixed model Bayesian and maximum likelihood inference methods. Podonominae is monophyletic and sister to Tanypodinae – the shared development of the larval ligula is synapomorphic and diagnostic. Tribe Podonomini is monophyletic with the inclusion of Trichotanypus; tribe Boreochlini is a grade. Monophyly is confirmed for the genera Podonomus Philippi, Podonomopsis Brundin, Podochlus Brundin, Archaeochlus Brundin and Austrochlus Cranston, Edward & Cook: Parochlus Enderlein becomes monophyletic through the inclusion of Zelandochlus Brundin (n.syn.) with its type species, P. latipalpis (Brundin) n.comb. The ‘mandibulate’Archaeochlus plus Austrochlus is monophyletic with nonmandibulate Afrochlus weakly supported as a member of, or sister to, the African Archaeochlus. Subtending this group is Lasiodiamesa, although it associates in some analyses with the sister group Tanypodinae. Generic relationships coincide with those proposed based on morphology, particularly as understood via all life history stages of some problematic (autapomorphic, adult-based) taxa. Divergence time analysis (beast) allows inference of Mesozoic diversification of higher taxa in Podonominae, of appropriate timing for fragmentation of Gondwana, post-African divergence, to have caused vicariance. Shallower nodes (within genera) imply both younger vicariance involving Antarctica and some recent dispersal, including southern to northern hemisphere movement in the New World. New Zealand taxa test controversial biogeographical relationships and show proximity to southern South America without direct Australian sister taxon pairs: dating implies persistence of midges through the ‘Oligocene’ bottleneck.