The phylogenetic relationships among the members of Macronematinae (Trichoptera: Hydropsychidae) have long been debated and often revised. Our study based on a large subunit (28S) nuclear ribosomal DNA (D2 expansion fragment; 464 base pairs) of gene sequences found all genera to be monophyletic except for the genus Polymorphanisus Walker, which produced two clades in accordance with its species groups established using morphological characters. Phylogenetic reconstruction based on mitochondrial cytochrome oxidase I (658 base pairs) found the same monophyletic relationships, however, except for the genera Polymorphanisus and Macrostemum Kolenati. The placement of the genus Leptonema Guérin-Méneville as the basal clade in the subfamily was also ruled out, which is consistent with previous morphological findings. The monophyly of two previously recognised tribes (Macronematini and Polymorphanisini) was not supported. We also found that the genera Centromacronema Ulmer, Baliomorpha Neboiss, and Macronema Pictet are most closely related, having three head setal warts on the vertex of the head and unsegmented inferior appendages of male genitalia as their synapomorphies. Our study supported the hypothesis of close relationship of the genera Amphipsyche McLachlan and Protomacronema Ulmer with the morphological synapomorphies: absence of a forewing discoidal cell and the presence of elevated head carinae on the larvae. Some notable evolutionary novelties in the structure of adults in various lineages of this subfamily include reduction of maxillae and labium, reduction and loss of a discoidal cell and evolution of a c-sc crossvein in each forewing, fusion of segments in each male inferior appendage, and evolution of dark colour patterns in the forewings. Also, the head setal warts, which are unique organs in Trichoptera, evolved towards a decreasing number in the subfamily. This first molecular phylogenetic study, covering most genera in Macronematinae and including an interpretation of 12 key evolutionary novelties, provides an important basis for resolving long-standing questions regarding phylogenetic relationships and classification of genera and species and helps lay a stronger foundation for inference of testable hypotheses about functional traits for species of this common and widespread subfamily.