The endangered Shivwits milkvetch, Astragalus ampullarioides, is a perennial, herbaceous plant. This Utah endemic was federally listed as endangered in 2001 because of its high habitat specificity and low numbers of individuals and populations. All habitat currently occupied by A. ampullarioides was designated as critical by the U.S. Fish and Wildlife Service in 2006 as a result of conservation litigation. We used AFLP markers to assess genetic differentiation among the seven extant populations and quantified genetic diversity in each. Six different AFLP markers resulted in 217 unambiguous polymorphic loci. We used multiple methods to examine any changes in population genetic structure in this species over time. Results indicate that A. ampullarioides had much higher gene flow among populations in the past, but has since fragmented into regional genetic units. These regions further fragmented genetically, and extant populations have differentiated through genetic drift. Populations had low levels of gene flow, even between geographically close populations. Rapid urban development reduces gene flow among regions and encroaches on populations of A. ampullarioides and remaining patches of unoccupied habitat. The genetic makeup of each of the extant populations should be carefully considered in management decisions such as population establishment or augmentation.