We investigated species boundaries between Juncus ensifolius, J. saximontanus, and their putative closest relative [or sister taxon] J. macrandrus, three members of a group of seven species of Juncus that are native to North America and have iris-like leaves. Juncus ensifolius and J. saximontanus have overlapping ranges in the central portion of Western North America, but J. ensifolius has a more northerly distribution, while J. saximontanus has a more southerly distribution. The distinctions between the two species have long been unclear, primarily due to the presence of individuals with a variable number of stamens, which is the primary character used to differentiate them. J. macrandrus is distinguished from our focal species by the length of its anthers, and is found only in the California floristic province, where the ranges of J. ensifolius and J. saximontanus overlap. We generated genotyping by sequencing data for 95 individuals of our two focal species and one individual from J. macrandrus, our putative outgroup. We used phylogenetic inference, evolutionary clustering, principal components analyses of morphological measurements, and other methods to investigate species boundaries in this group. We found that introgression with closely related species in the group such as J. macrandrus, but not between J. ensifolius and J. saximontanus, is a primary driver of uncertainty about species distinctions. We also found evidence for an independently evolving lineage in J. saximontanus that may deserve recognition at the species level. We determined that J. saximontanus and J. ensifolius are distinct species and can be recognized based on stamen number as well as number of heads per inflorescence. We propose that individuals with intermediate characters are most likely the result of hybridization with J. macrandrus or another closely related species.