Random amplified polymorphic DNA (RAPD) analysis was used to characterize genetic diversity and genetic distinctiveness of Andropogon gerardii from remnant Arkansas prairies. Six oligonucleotide primers, which generated 37 RAPD bands, were used to analyse 30–32 plants from six Grand Prairie populations, Baker Prairie (Arkansas Ozarks), two Illinois prairies and two cultivars. Genetic diversity of the Arkansas remnants ranged from 82.7 to 99.3%, with 89% of the total genetic variation within and 11% among populations. The partitioning of genetic variation was consistent with that reported for other outcrossing perennial grasses, using the more conservative allozyme markers. Principal component analysis indicated a northern and southern association within Arkansas’ Grand Prairie. Although there was no genetic structuring at the landscape level, the Illinois prairies and cultivars were different from all Arkansas prairies tested. There was significant within-population structuring in four of the seven Arkansas remnants, with a negative relationship between genetic similarity and geographical distance. The three nonstructured populations were from a linear railroad remnant, suggesting different population-level dynamics from nonlinear prairies. The results of this study indicated that small isolated remnant big bluestem populations were not genetically depauperate and that genetic relationships among populations could not be predicted solely on geographical proximity.