The invasive species cogongrass (Imperata cylindrica L. Beauv.), was accidentally and intentionally introduced into the United States, and has adapted to a wide range of habitats, including pastures, rangeland, reclaimed mining sites, forests, roadsides and other rights-of-ways, and recreational and natural areas. To better understand the biology, species composition, and systematic taxonomy of the reservoir of genetic diversity in Imperata sp. that has been handed down through decades in the United States, six morphologically distinct populations were collected from Alabama (Mobile and north Alabama), Louisiana, and Florida. Populations composed of Ornamental ‘Red Tip' or ‘Red Barron' and the ‘Hybrid' were obtained from the University of Florida, Gainesville. Using AFLP markers, gene diversity, molecular variance, and phenetic relationship were estimated among and within populations.  Three AFLP primers generated a total of 191 markers of which 184 (96%) were polymorphic. The analysis of molecular variance (AMOVA) revealed that 69% (P < 0.05) of the total variance was within populations, suggesting the cross-pollinated nature of Imperata sp. while among populations variance component was estimated to be 34% (P < 0.05). Gene diversity in the populations of ‘Red Barron' and ‘Hybrid' was estimated to be 0.24 and 0.31, respectively. Principal component analysis and cluster analysis separated all clones into 4 major groups. Population of ‘Red Barron' did not differ from that of ‘Hybrid' with the AFLP profile, though significant differences were noted at the morphological level. We suggested that these populations are closely and genetically related. The origin of the ‘Hybrid' should be investigated.