The amphitropical Trifolium depauperatum Desv. species complex (Fabaceae) is a group of closely related clovers with a disjunct native distribution in Chile and western North America. Based on the most recent treatment by Vincent and Isely in 2012, the species complex includes two species, one of which contains three varieties. Historically, the taxonomy of this species complex has been unstable; therefore, we performed a morphological and molecular analysis from herbarium specimens and fresh tissue to further explore taxonomic delimitations. Multivariate and cluster analyses were performed on the morphological data. Bayesian and Maximum Parsimony phylogenetic analyses were performed on the molecular data. Both data sets support the recognition of four taxa: T. depauperatum var. depauperatum, T. depauperatum var. amplectens (Torr. & A.Gray) Rattan, T. depauperatum var. truncatum (Greene) J.S.Martin ex Isely, and T. hydrophilum Greene. We designate three new lectotypes and one epitype, and provide a key to taxa, synonymy, descriptions, and distributional information for each.