Abstract Premise Juncaceae has needed taxonomic revision for some time. Specifically, the genus Juncus s.l. is known to be paraphyletic because five small southern‐hemisphere genera have been shown repeatedly to be nested within it. In 2022, a new classification was proposed, based on phylogenies built from one nuclear and three plastid regions sequenced across much of Juncaceae, meant to resolve the paraphyletic nature of Juncus s.l. It created six new genera and was criticized on the basis that the genera proposed are not necessarily monophyletic, given the limited nature of the phylogenetic analyses available and the fact that the generic circumscriptions draw heavily on the morphology‐based classifications in the latest monograph of Juncaceae from 2002. Methods We used the Angiosperms 353 target capture probe set to assemble a data set consisting of hundreds of plastid and nuclear loci to assess the monophyly of the newly proposed genera of Juncaceae. Results The proposed genera mostly represent monophyletic groups, but the proposed genus Juncinella is nested within the proposed genus Boreojuncus . Additionally, Juncinella capitata was placed as sister to either Luzula or Oreojuncus and should be recognized as a monotypic genus. Finally, Australojuncus cyperoides and Verojuncus chlorocephalus were recovered outside of their morphologically assigned genera and require further investigation to be placed confidently. Conclusions We proposed taxonomic revisions to rectify the stated issues, but further research is necessary, particularly to correctly place the South African annual taxa in Juncus s.l.