The Tennessee milk vetch, Astragalus tennesseensis Gray, and the leafy prairie clover, Dalea foliosa (Gray) Barneby, are cedar glade endemics with disjunct populations in formerly glaciated Illinois dolomite prairies. We explored the effects of geographical isolation on the levels and distribution of genetic variation in these rare species. Isozyme analyses were conducted using leaf tissue from 19 populations (429 individuals) of Astragalus tennesseensis and 10 populations (240 individuals) of Dalea foliosa throughout their geographical ranges in Illinois, Tennessee, and Alabama. Across all A. tennesseensis populations sampled, 13 out of 15 loci (87%) were polymorphic, (14-57% within populations), averaging 2.6 alleles per polymorphic locus. In D. foliosa, 11 out of 20 (55%) loci were polymorphic, (0-30% within populations), averaging 2.0 alleles per polymorphic locus. Across loci, levels of observed and expected heterozygosity in A. tennesseensis (H-O = 0.103 and H-E = 0.121) were more than twice that found in D. foliosa (H-O = 0.037 and H-E = 0.043). For both species, levels of heterozygosity were highest in Tennessee and lowest in Illinois, where levels half that found in Tennessee. Differentiation among populations within geographical regions (G(STC) = 0.161 and 0.145 for A. tenneseensis and D. foliosa, respectively) was lower than when not clustered by regions (G(ST) = 0117 and 0.441). In A. tennesseensis, the majority of species-level genetic diversity was contained within populations (H-S = 0. 141 as compared to total diversity H-T = 0. 179), but in D. foliosa, the opposite was true (H-S = 0.060 as compared to H-T = 0. 186). Given the high degree of differentiation among geographical regions, particularly in formerly glaciated Illinois, conservation strategies for these species should include consideration of their geographical affinities.