Cladistic analysis of rbcL nucleotide sequences was applied to 58 taxa representing most subgenera and sections of Luzula and Juncus, chosen to reflect morphological and geographical diversity of both genera. Additionally, representatives of all other genera of the Juncaceae and two taxa from the Cyperaceae were included. Phylogenetic trees were constructed using parsimony with Prionium serratum as outgroup. The dataset has 190 parsimony informative sites. The analysis yielded more than 332,400 equally parsimonious trees (length 620, CI=0.47, RI=0.82). A jackknife analysis revealed several well-supported clades. Luzula is monophyletic and Juncus is non-monophyletic. Each of the generally accepted subgenera of Juncus, subg. Juncus and subg. Agathryon, form a clade, but their circumscription differs from the traditional views. The subgenera recognized in Luzula remain mainly unresolved. A well-supported clade is represented by an assemblage of representatives of five genera and species distributed in the Southern Hemisphere: Juncus capensis and J. lomatophyllus (both from section Graminifolii), Rostkovia, Distichia, Marsippospermum, and Patosia.