We have investigated the local and regional scale genetic structure of Siberian primrose (Primula nutans) populations in Northern Europe. The genetic diversity and structure of fifteen populations sampled from the Bothnian Bay in Finland, the Barents Sea in Norway and the White Sea in Russia were assessed using eleven microsatellite markers. We investigated the distribution of genetic variation within and between populations, and studied the local genetic structure using spatial autocorrelation analysis. We found very low genetic and allelic diversity in the Bothnian Bay and Barents Sea populations, and only slightly higher in the White Sea population. The level of genetic differentiation between the regions was very high, whereas differentiation between the populations within the regions was moderate. We found no spatial structuring of populations in any region suggesting efficient dispersal on a local scale. Clonal reproduction seemed to have no effect on genetic structure.