Johnsongrass (Sorghum halepense (L.) Pers.) is an invasive, polyploid grass found throughout disturbed and agriculture areas of temperature, subtropical, and tropical regions. This species is thought to be an allotetraploid formed through the hybridization of sorghum (Sorghum bicolor (L.) Moench) and Sorghum propinquum (Kunth) Hitchc. Subsequent hybridization back to S. bicolor followed by introgression into Johnsongrass populations has led to the introduction of weedier traits in some germplasm. Since its introduction into the United States in the early 1800s and secondary introduction into Arizona sometime later, Johnsongrass has spread throughout much of the Southeast, lower Great Plains, portions of the Midwest, Southwest, and California. The movement of this invasive has been facilitated by the transport of agricultural products and the development of major railway and highway systems where Johnsongrass thrives in the disturbed areas surrounding fields, railroads, and highways. In this study, we sampled and isolated whole genomic DNA from approximately 300 individuals from more than 50 populations across the United States. Using low-coverage whole genome shotgun Illumina sequencing, we assembled whole chloroplast genomes for each sample. We also assembled whole chloroplast genomes from similar data found in the NCBI SRA for multiple Sorghum species including over 50 S. bicolor lines. Using these data, we reconstructed a maximum likelihood phylogeny using other members of the Andropogoneae as outgroups. We also constructed a chloroplast haplotype map focusing on S. arundinaceum (S. bicolor var. arundinaceum), S. bicolor, S. halepense, and S. propinquum chloroplast genomes to identify patterns of similarity across US populations. We found that the chloroplast diversity of US Johnsongrass falls into two main groups: one allied with S. bicolor and S. propinquum and the other with unique haplotypes and no clear relationship to putative parental haplotypes. There was no clear relationship between geographic origin of specimens and their chloroplast haplotypes. In some cases, identical or nearly identical haplotypes were found in populations from across the country, suggesting potential long-distance dispersal. Similarly, chloroplast haplotypes were found to be identical to those seen in improved sorghum lines, suggesting recent hybridization and chloroplast capture of these sorghum haplotypes into US Johnsongrass populations. This works demonstrates that though widespread dispersal and hybridization to sorghum have likely shaped the genetic variation across populations of Johnsongrass, there remains a subset of chloroplast haplotypes that may represent unique genetic diversity. Future work will investigate the nuclear genomes of these samples to better describe this diversity and how variation in diploidization may drive adaptation into new environments.