Chloroplast DNA (cpDNA) sequences are appropriate for studying intraspecific phylogeography.  Comparing cpDNA phylogeny with different cytotypes provides insights into the origin and establishment of polyploid species. In this study chloroplast haplotype variation is explored in 54 populations of prairie cordgrass, using 9 non-coding chloroplast regions.  These chloroplast analyses were combined with the cytotype surveys of prairie cordgrass to infer the phylogeography and to elucidate the origin of the different cytotypes.  In this study, three haplotypes, prairie cordgrass G1 (PCG1), prairie cordgrass G2 (PGG2), and prairie cordgrass G3 (PCG3), were identified.  In general, related haplotypes were strongly associated with geographic distribution.  Prairie cordgrass G1 haplotypes have been identified from East North Central to New England regions of the U.S., where polyploid (tetraploid, hexaploid, and octoploids) prairie cordgrass populations were found.  Prairie cordgrass G3 haplotypes were distributed in octoploids in ND, SD, and MN, while PCG2 haplotypes were mostly identified in octoploids and few in tetraploids occuring in south part of SD, IA, and MO.