Genetic diversity throughout the rapeseed (Brassica napus ssp. napus) primary gene pool was examined by obtaining detailed molecular genetic information at simple sequence repeat (SSR) loci for a broad range of winter and spring oilseed, fodder and leaf rape gene bank accessions. The plant material investigated was selected from a preliminary B. napus core collection developed from European gene bank material, and was intended to cover as broadly as possible the diversity present in the species, excluding swedes (B. napus ssp. napobrassica (L.) Hanelt). A set of 96 genotypes was characterised using publicly available mapped SSR markers spread over the B. napus genome. Allelic information from 30 SSR primer combinations amplifying 220 alleles at 51 polymorphic loci provided unique genetic fingerprints for all genotypes. UPGMA clustering enabled identification of four general groups with increasing genetic diversity as follows (1) spring oilseed and fodder; (2) winter oilseed; (3) winter fodder; (4) vegetable genotypes. The most extreme allelic variation was observed in a spring kale from the United Kingdom and a Japanese spring vegetable genotype, and two winter rape accessions from Korea and Japan, respectively. Unexpectedly the next most distinct genotypes were two old winter oilseed varieties from Germany and Ukraine, respectively. A number of other accessions were also found to be genetically distinct from the other material of the same type. The molecular genetic information gained enables the identification of untapped genetic variability for rapeseed breeding and is potentially interesting with respect to increasing heterosis in oilseed rape hybrids.