The levels of genotypic and genetic variation were estimated in six natural populations of arctic bramble (Rubus arcticus L. subsp. arcticus) in Finland. Using three primer combinations, a total of 117 amplified fragment length polymorphisms (AFLP) were found. The results were highly reproducible and allowed identification of 78 genets among the 122 plants of arctic bramble studied. Genotypic variation measured as Simpson index (D) was high in all populations, ranging from 0.72 to 0.94. Also, the level of genetic variation measured as Shannon index was relatively high in all populations, ranging from 0.19 to 0.32 (average 0.26). The high levels of genetic diversity indicate that sexual reproduction has played a significant role in these populations. The hierarchical analysis of molecular variance (AMOVA) partitioned 48% of the genetic variation among populations, suggesting a high level of population differentiation and a low level of interpopulation gene flow. Genetic diversity among ten currently grown cultivars of arctic bramble and hybrid arctic bramble (R. arcticus subsp. arcticus x R. arcticus subsp. stellatus) was large, and the subspecies were clearly distinguished from each other based on the AFLP marker data.