The population genetic structure of invasive weed species contributes to our understanding of the life story and evolutionary processes associated with invasion.  Cogongrass (Imperata cylindrica L. Beauv.), introduced into the United States shortly after the turn of the twentieth century, is an aggressive, invasive weed species which colonizes a diverse range of habitats including pastures, rangeland, forests, roadsides and other rights-of-ways, and recreational and natural areas.  Genetic structure and genotypic diversity were assessed from 24 natural populations of I. cylindrica collected in two geographic regions, western and eastern Alabama.  Three AFLP primer pairs detected a total of 240 markers of which 236 (98%) were polymorphic.  Hierarchical analysis of molecular variance indicated that only 6.9% (Φ_CT = 0.07, P > 0.05) of the variance in allelic frequencies was partitioned at the among-region level.  Among populations captured 57.2% (Φ_ST = 0.64, P < 0.05) of the total genetic variation while the within population component was estimated to be 35.8 % (Φ_SC = 0.62, P < 0.05), suggesting that the dual mode of reproduction, asexually through rhizomes and sexually by seed, has an influence on the genetic structure of I. cylindrica populations. High levels of genetic differentiation were found between populations regardless of the geographic distance separating them.  here is no evidence for isolation-by-distance for natural population.  We hypothesized that population differentiation and genetic isolation is driven by anthropogenic dispersal. Gene flow (Nm) inferred from Φ-statistics, describing the genetic differentiation between populations, ranged from 0.01 to 4.5. Private alleles were observed in one population out of 24 and accounted for 19.6% of the total number of alleles, indicating its considerable difference of the genetic constitution. According to principal component analysis and cluster analysis, this population was separated from the rest. Overall, populations showed a low gene diversity value (H_T = 0.11).