Knowledge of genetic variation and population structure is critically important in the conservation of endangered species. The level and partitioning of genetic variation in the narrow endemic Astragalus jaegerianus was investigated using DNA sequence data and AFLP markers. The DNA sequence data for the cpDNA trnL-F and nrDNA ITS regions were monomorphic for A. jaegerianus but polymorphic for two congeners, which suggest A. jaegerianus is genetically depauperate. On the other hand, the genome-wide survey using AFLP markers revealed substantial gene diversity (0.2660) and significant population structure (global F_ST  =  0.133, p < 0.01). This level of gene diversity and its partitioning among populations is comparable to patterns for geographically widespread species. These findings also challenge the hypothesis that levels of gene diversity are best predicted by population size. In this case, levels of gene diversity within populations are significantly correlated with population density, while geographic distances and gene flow explain patterns of population structure. These results suggest a breeding strategy for A. jaegerianus as a facultative outcrosser that relies more on outcrossing in areas of high plant density and less so in areas of low plant density. Conservation measures are recommended that include monitoring population genetics, numbers of individuals, and population densities.