Relationships within Schoenoplectus and Schoenoplectiella are largely unknown and the phylogenetic positions of these genera relative to the other four genera in Fuireneae and clade of Cypereae are unclear. A few studies with sparse or localized sampling have added valuable insights, but a North American sampling and a broad global perspective are needed. To generate a more robust phylogenetic hypothesis, we increased the number and breadth of taxon sampling in Schoenoplectus and Schoenoplectiella, including all constituent species in North America, all genera in Fuireneae, and strategically sampled genera in Cypereae. Phylogenetic relationships were estimated using DNA sequences from the nuclear ribosomal ITS region, chloroplast DNA trnL intron and trnL-trnF intergenic spacer region, and partial chloroplast DNA ndhF coding region and parsimony, likelihood, and Bayesian analyses. The proposed phylogeny reveals Pseudoschoenus, Schoenoplectiella, and Cypereae are supported as a clade, and Schoenoplectiella is paraphyletic and sister to Pseudoschoenus. Schoenoplectus is monophyletic, sister to Actinoscirpus. Schoenoplectus sections Schoenoplectus and Malacogeton were resolved; comprehensive sampling in Schoenoplectus section Schoenoplectus and unclear placement of S. californicus suggests the need to examine formerly recognized section Pterolepis. The proposed phylogeny supports the erection of sections in Schoenoplectiella, but indicates further morphological and molecular data is needed for section diagnoses. Two Cypereae taxa previously resolved in a Schoenoplectiella clade were included in this analysis: Scirpoides varia resolved in a clade with Cypereae taxa, and Isolepis humillima resolved within Schoenoplectiella. Results from the phylogenetic hypotheses support a need to revisit the generic placement of Isolepis humillima and revise Fuireneae to resolve tribal paraphyly.