Imperata cylindrica (cogongrass) is an invasive weed long established in the southeastern US, and considerable effort is devoted to its control. Two native species, I. brevifolia (California satintail) and I. brasiliensis (Brazilian satintail), also occur in the US, and the latter is sympatric to cogongrass. Certain Imperata morphotypes growing in the field are difficult to identify. To clarify their identity, inter-simple sequence repeats (ISSRs) were used to assess genetic differentiation among eight populations in the US representing Brazilian satintail, California satintail, three potential morphotypes of cogongrass, and three unknowns. Samples preserved in 95% ethyl alcohol and silica-gel did not produce repeatable band patterns, so DNA from fresh leaves was extracted and analyzed by polymerase chain reaction (PCR) amplification. Results indicate that California satintail (D = 0.67), a commercial cogongrass cultivar (D = 0.66), and a short-hairy morphotype of cogongrass (D = 0.65) were the most distinctive operational taxonomic units (OTUs) compared. The unweighted pair group method with arithmetic mean (UPGMA) dendrogram showed two well-supported clusters of taxa containing Brazilian satintail (Bootstrap value = 96%) and the tall morphotypes of cogongrass (Bootstrap value = 83%), respectively. Among the morphotypes of cogongrass analyzed, the tall-hairy and tall-glabrous plants formed a cluster from which the short-hairy morphotype and the cultivar were genetically divergent. Our results refute taxonomic arrangements placing Brazilian satintail as a synonym of cogongrass.