The extranuclear DNA containing organelles (e. g., chloroplast and mitochondria) of any particular plant species are extremely useful tools in assessing genetic variation, resolving phylogenies (Timothy et al. 1979; Gielly and Taberlet 1994; Aizawa et al. 2007) and serving as vectors for transgene expression (Nakahira and Shiina 2005; Lu et al. 2006; Remacle et al. 2006; Farre et al. 2007; Hanson et al. 2012). In particular with plant species that have tetraploid genomes and higher (many of the grasses), using nuclear markers to compare across ploidy levels are difficult in these populations because gene copy number and allele frequencies are affected under polysomic inheritance (Young et al. 2011). As an alternative in these complex grassland ecosystems, chloroplast genome sequences can possibly provide a greater understanding of the evolutionary processes that have taken place during establishment from a comparative approach of isolated subpopulations (Young et al. 2011). As noted, switchgrass accessions primarily consist of lowland and upland ecotypes (Porter 1966) where lowland accessions are predominantly tetraploids (2n=4x=36), while upland accessions are octaploids (2n=8x=72) (Bouton 2007) making population genetic comparisons difficult because of a variance of ploidy levels affecting orthologous loci. In most angiosperms, the chloroplast genome consists of a quadripartite structure that includes a large single copy region (LSC) and a small single copy region (SSC) flanked by two inverted repeats, and maintains a pattern of maternal inheritance (Soltis et al. 1990; Faure et al. 1994; Vivek et al. 1999) making it an ideal genetic marker for phylogenetic studies (Chung et al. 2003; Liu et al. 2012). Previous studies aimed at discriminating ecotypes was focused on an RFLP marker in the rbcL gene (Hultquist et al. 1996), but the lack of comprehensive data points represents a need for more robust analysis. At present, two switchgrass chloroplast genomes from individuals representative of the lowland (Kanlow) and upland (Summer) ecotypes (Young et al. 2011) have been sequenced and compared to identify a 21 bp insertion in the Summer ecotype at the C-terminal region of rpoC2 gene that is a reproducible marker for resolving ecotypes (Young et al. 2011).