Relationships among genera and more inclusive clades of net-winged midges (Diptera: Blephariceridae) have been difficult to resolve with confidence. Part of this difficulty reflects common and extreme adaptive constraints on the immature stages, which reside in torrenticolous habitats. Previous phylogenetic hypotheses have provided relatively robust support for monophyly of the subfamilies Edwardsininae and Blepharicerinae, and, to a lesser extent, the tribe Apistomyiini and various generic groupings. In general, monophyly of the tribes Paltostomatini and Blepharicerini, and the relationships between these tribes and apistomyiines have been much more contentious. To test hypotheses on relationships between subfamilies, tribes, and genera of Blephariceridae, we examined exemplars of nearly all genera for morphological characters, and two-thirds of known genera for molecular characters. The latter included multiple exemplars of all subfamilies and tribes, and usually at least two species from each exemplar genus. Molecular data were primarily from a new, rapidly evolving, nuclear-encoding gene (“tuftelin-interacting protein”). Our analysis provided support for new and existing hypotheses about relationships among net-winged midges. Data showed strong support for both subfamilies and a combined Paltostomatini + Apistomyiini. Relationships within these tribes and the Blepharicerini included a range of support values, with paltostomatines and basal blepharicerines being the least resolved.