Heather plants were collected from 34 populations in Great Britain, which differed according to their geographical location and associated management histories. Comparisons of differential grazing regimes were made across 10 sites in the first year of study, whereas the influence of differential burning regimes was considered at four sites during the second year. The extent of genetic variation, both within and between the selected heather populations, was examined using polymerase chain reaction (PCR)-based DNA fingerprinting methodologies. Initially, high genetic variation within populations obscured differences between populations. Heather stands that were geographically close proved to be genetically similar. Site latitude and longitude were strongly associated with genetic differences between heather populations; however, a range of grazing and burning management treatments had no consistent effect upon genetic diversity. The results represent the first national survey of genetic variation at the DNA level within UK populations of this important heathland species. They provided insights into the genetic structure of heather-dominated heathlands, revealing a lack of clonal dominance within populations, but rather a much more varied genetic makeup than might have been expected given the species’ ability to propagate vegetatively. The processes that influence genetic diversity in heather populations are discussed, and the potential role of molecular techniques in heathland conservation is considered.