Astragalus lentiginosus is a polymorphic species that occurs in geologically young habitats and whose varietal circumscription implies active morphological and genetic differentiation. In this preliminary study, we evaluate the potential of amplified fragment length polymorphism (AFLP) markers to resolve infraspecific taxa in three varieties ofAstragalus lentiginosus. Distance-based principle coordinate and neighbor-joining analyses result in clustering of individuals that is congruent with population origin and varietal circumscription. Analysis of molecular variance of two Oregon varieties demonstrates that varietal categories account for 11% of the total variance; in contrast, geographic proximity does not contribute to the total variance. AFLPs demonstrate an ability to discriminate varieties ofA. lentiginosus despite a potentially confounding geographic pattern, and may prove effective at inferring relationships throughout the group.