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Phylogenetic relationships of Juncaceae and related families of Cyperales were investigated using DNA sequence data from the plastid rps16 intron, trnL intron, and trnL–F intergenic spacer. Results using parsimony analysis of the aligned matrices find Juncaceae and Cyperaceae to be monophyletic families, which form a clade sister to a monophyletic Thurniaceae that includes Prionium (Prioniaceae), all three clades with 100% bootstrap support. Within Juncaceae, the genus Luzula is monophyletic with 100% bootstrap support and sister to the rest of Juncaceae. Further groupings within the family indicate that the genus Juncus may be monophyletic only with the inclusion of the single-flowered genera of Juncaceae (Distichia, Oxychloe, Marsippospermum, and Rostkovia; sequences of Patosia were not included). Major groupings within Juncus are supported by the morphological characters of septate or non-septate leaves and the presence or absence of bracts subtending the flowers, which have been used to define subgenera and sections within Juncus.