Two major obstacles to quantifying biodiversity are reticulate evolution and the evolution of genetically distinct but morphologically overlapping cryptic species. The Spiranthes cernua species complex (Orchidaceae) has defied satisfactory species delineation, often described as intractable, due to morphological variability within species, overall morphological similarity between species, possible cryptic speciation, and suspected hybridization. Weutilized low copy nuclear, nuclear ribosomal, and chloroplast molecular phylogenetic datasets, in addition to expansive field and herbarium research, to clarify long-standing questions regarding species boundaries within the S. cernua species complex. Our results justify: 1) narrowing the concept of S. cernua; 2) the description of a new cryptic species, Spiranthes arcisepala; 3) the description of a new geographically restricted species of cryptic and ancient hybrid origin, Spiranthes niklasii (S. cernua × S. ovalis); 4) a new combination for a biogeographically specific cryptic species of ancient hybrid origin, Spiranthes incurva (S. cernua×S. magnicamporum); and 5) the description of a new localized hybrid, Spiranthes ×kapnosperia (S. cernua × S. ochroleuca). We also propose formal synonymization of federally endangered Spiranthes parksii under S. cernua s. s. Our research clarifies species boundaries within this challenging group, and is the first to use molecular phylogenetic data to support hybridization as an evolutionary force within the S. cernua species complex.