Pennisetum setaceum (Poaceae) is a perennial bunch grass that invaded the United States during the 20th century and is highly invasive in Hawaii, moderately invasive in Arizona, and not yet invasive in southern California. Pennisetum setaceum is apomictic, a condition that is normally associated with low genetic variation within populations, but even moderate levels of genetic variation among populations could account for differences in invasiveness. To determine whether genetic factors are causing the variable invasion success, we used Inter-Simple Sequence Repeat markers (ISSRs) to examine genetic variation in populations from the three areas. Screening of 16 primers revealed no genetic variation within any population or between any geographical areas, a pattern consistent with complete apomixis. Variation in invasion success appears unrelated to genetic differences among populations. Differences in the seasonal timing of rainfall among the regions may be the cause of variable invasiveness of fountain grass. Alternatively, differences in timing of introduction or duration of lag phase may have limited invasiveness in Arizona and southern California.