The Utricularia dichotoma Labill. complex is a morphologically and ecologically variable group of closely related taxa with a mostly temperate distribution across New Zealand, New Caledonia and Australia. Taxonomic boundaries within the complex have been the subject of speculation, with several previously recognised species being synonymised after a nomenclatural revision. We sampled 296 populations representing all known taxa; 223 accessions were used in the full phylogenetic analysis based on two non-coding chloroplast regions (rps16, trnD–T) and two nuclear ribosomal spacers (external transcribed spacer, ETS; internal transcribed spacer-1, ITS-1), whereas the remaining accessions were identified by using ITS-1 barcodes. We found strong support for a paraphyletic U. dichotoma, with accessions matching the type material of that name grouped within a polytomy that includes clades containing accessions of U. monanthos Hook.f and U. novae-zelandiae Hook.f. Specific statuses for five recently described species previously included in U. dichotoma s.l. do not fall within this polytomy, nor do the two species U. oppositiflora R.Br. and U. speciosa R.Br. resurrected from synonymy of U. dichotoma. All sampled accessions from New Zealand form a single clade within U. dichotoma as recognised here. We here propose that seven clades recovered here be recognised as subspecies, and describe eight new subspecies, including two new combinations. We also propose that the monophyletic clade sister to U. beaugleholei Gassin be assigned to subspecies rank under that name.