Chloroplast DNA (cpDNA) sequences are very useful for studying genetic variation among populations.  Comparing cpDNA haplotypes have provided valuable insight into the establishment and migration of polyploid populations.  In this study, cpDNA haplotype variation was surveyed within populations of prairie cordgrass using two non-coding chloroplast regions.  One population, located in North Dakota, consists of a single cytotype.  The other population, located in Illinois, is a mixed cytotype population.  It was discovered, that chloroplast genome variation existed in the ND population.  In one variant, a base substitution and deletion were observed in 30.6% of the population; while independently, a second deletion was observed in 28.6% of the population.  No cpDNA variation was observed within the IL population.  However, the IL population cpDNA was observed to be the same as one of the variants found in ND.  Future populations are being analyzed to assess total cpDNA variability within PCG populations.  This information will be critical in using cpDNA for phylogenetic studies.