Grasses and grasslands are among the most important biological systems on the planet, providing habitat for wildlife, forage for grazers, and grain for animal and human consumption. Bouteloua eriopoda (black grama) is a key species of the grasslands that once covered large parts of the Northern Chihuahuan Desert. Over the last 150 years these grasslands have experienced a significant reduction in geographic coverage as a result of creosote and mesquite shrubland encroachment. The genetic consequences of reduced population size and fragmentation on black grama, or other grasslands, remains unclear. However, research on other wind pollinated plant species suggests that these phenomena result in reduced genetic variation with various potential long-term consequences. In extreme cases a genetic bottleneck can occur, leading to inbreeding depression. Here we present the development of microsatellite and AFLP-based marker systems in black grama for future investigations focusing on spatial patterns of genetic diversity in black grama. Microsatellite loci were developed using an established restriction endonuclease and di/tri-nucleotide repeat enrichment protocols followed by subsequent extensive screening of candidate loci. In addition, six selective AFLP primer combinations were screened for reproducibility and recovery of polymorphic loci. Preliminary results from the analysis of ten individuals for each of five populations of black grama identify nine microsatellite loci that amplify well. However, little genetic diversity is observed within or between populations with these loci. AFLP analyses across the same populations have identified three selective primer combinations (MseI-CTA/EcoRI-AT, MseI-CTA/EcoRI-TT, and MseI-CTA/EcoRI-AC) that amplify well and that together result in 275 polymorphic loci from 376 total loci (73% polymorphic). In contrast to the genetic variation observed with the available microsatellite markers, the preliminary AFLP data identify considerably more variation within and between populations.