Fassett's locoweed (Oxytropis campestris var. chartacea, Fabaceae) is an endangered perennial endemic to Wisconsin. Patterns of genetic variation within and among six remaining populations and their relationship to other members of the O. campestris complex were analysed using AFLPs from 140 accessions across northern North America. Within-population measures of genetic diversity were high (mean expected heterozygosity HE = 0.16; mean nucleotide diversity pi = 0.015) compared with other herbaceous plants. Estimates of among-population differentiation were low (FST = 0.12; PhiST = 0.29), consistent with outcrossing. Genetic and geographical distances between populations were significantly correlated within Fassett's locoweed (r2 = 0.73, P < 0.002 for Mantel test) and O. campestris as a whole (r2 = 0.63, P < 0.0001). Individual and population-based phylogenetic analyses showed that Fassett's locoweed is monophyletic and sister to O. campestris var. johannensis. Morphometric analyses revealed significant differences between Fassett's locoweed and populations of var. johannensis. The first chromosome count for Fassett's locoweed indicates that it is tetraploid (2n = 32), unlike hexaploid var. johannensis. High within-population diversity and relatively low among-population differentiation are consistent with populations of Fassett's locoweed being relicts of a more continuous Pleistocene distribution. Our data support the continued recognition of Fassett's locoweed and protection under federal and state regulations. High levels of genetic diversity within populations suggest that maintain-ing the ecological conditions that favour the life cycle of this plant may be a more pressing concern than the erosion of genetic variation.