These data were compiled to support effective conservation for species within Astragalus sect. Humillimi. Two species, A. cremnophylax var. cremnophylax and A. humillimus are federally listed as endangered taxa. The data provided herein were used to resolve the relationaships among taxa, the population structure within taxa, and genetic diversity within taxa. The data are provided in a STRUCTURE-formatted file that includes taxa, individuals, sampling localities, and the genotype scores per individual for 690 Amplified Fragment Length Polymorphisms (AFLPs).