Lupinus polyphyllus and L. wyethii are closely related members of a species complex widely distributed in western North America. Principal components analysis of morphological characters showed that these two taxa intergrade extensively, with many intermediate forms occurring. DNA sequences of the internal transcribed spacer (ITS) region in 28 individuals were variable at five base positions, both within and between taxa; some of these sequences have also been reported from related species. Molecular variation showed a geographic pattern but did not strongly reflect morphological differences. Morphological features that have been used to separate species in this group may primarily reflect local adaptation rather than underlying phylogenetic divergence. The lack of clear differentiation between these two lupines suggests that they are best treated as varieties of a single species, L. polyphyllus.