Switchgrass (Panicum virgatum L.) is a native to US Prairies and is productive in areas marginal for cropland production. It has high biomass production potential thus is an excellent choice as a sustainable energy crop. Genomic tools for switchgrass are very limited and need to be developed. A mapping population from a cross between clonal genotypes from ‘Alamo’ (lowland type; ID # AP13) and ‘Summer’ (upland type; ID #VS16) was initially developed at the University of Georgia and has now been expanded and maintained at the Noble Foundation. Microsatellite markers developed from conserved grass (CG), tall fescue (TF) and switchgrass ESTs were assessed on parents and a subset of the mapping population. The primer amplification varied significantly with 78% of the CG primers and 14% of the TF-EST-SSRs produced clean SSR-type amplification products in switchgrass population. On an average, each primer pair produced 1.7 fragments. Only 42% of the amplified fragments from both marker systems fell within the expected size range (105 – 450 bases) and remaining 58% were fragments with higher molecular weight. Polymorphism rates were higher in TF-EST-SSRs (86%) compared to CG-EST-SSRs (79%). Loci segregating in the switchgrass mapping population were grouped as loci segregating from the female parent (AP13, 55%), the male parent (VS16, 24%), and both parents (21%). A higher rate of marker segregation from the lowland genotype was evident over the upland genotype. Details of the marker development, amplification, and segregation in switchgrass population will be presented.