Trillium ovatum Pursh is a widespread species of the Pacific Northwest, northern California, and Rocky Mountain region that has been noted for its morphological variability. Here we present data from analysis of DNA sequence variation to show that this taxon includes four distinct species as currently circumscribed. The focus of this study was the comparison of the narrowly distributed T. ovatum subsp. oettingeri Munz & Thorne and the widespread T. ovatum s. s. Analyses of DNA sequence data for the nuclear ribosomal ITS and partial sequences of the plastid ycf1 and ycf2 genes from multiple samples of each were coupled with observations from morphology and floral scent to document that these are distinct species. The two species differ in proportional size of flower parts (larger in T. ovatum) and floral scent (more intense in T. ovatum). To update the taxonomy, T. oettingeri (Munz & Thorne) Renner comb. nov. is proposed. With a restricted range in the Klamath Mountains and part of the Cascade Range in northern California, T. oettingeri is a species of potential conservation concern. DNA sequence analyses also indicated that samples currently considered to be T. ovatum from the Rocky Mountain region represent a distinct species, for which T. stenosepalum (R.R.Gates) A.J.Wright comb. nov. is proposed. This taxon was somewhat surprisingly placed as a close sister group to T. oettingeri. Phylogenetic estimations further placed the overlooked T. crassifolium Piper as sister to T. nivale Riddell of the eastern U.S., a result supported by aspects of morphology and habitat. Trillium crassifolium from Washington, Idaho, and Oregon is not closely related to the sympatric Trillium ovatum, with which it has been placed in synonymy.