Three major simple sequence repeat (SSR) groups were identified in a global collection of 164 oilseed Brassica rapa based on allelic diversity at loci: SSR group 1 (south Asia, predominantly from India, Pakistan, and Nepal); SSR group 2 (predominantly southern and eastern Europe with mostly winter and semi-winter types); and SSR group 3 (northern Europe, mostly from Germany, and many of unknown origin). Nine outliers from several regions were placed in a fourth SSR group, which had the highest allelic diversity per accession of all SSR groups. Analysis of molecular variance of SSR data supported four groups but indicated that genetic variance within populations was high (84%) compared with variance between populations. Flowering habit was classified as winter, spring or semi-winter type, and pollination control as self-incompatible or self-compatible. These phenotypes were distributed across each of the three SSR groups and outliers, although most SSR group 1 accessions were self-compatible spring types, and winter types were mainly from SSR groups 2 and 3. Two SSR sub-groups were present among Indian accessions, both of which contained brown-seeded types, but only one sub-group contained yellow-seeded types (most likely yellow sarson). Eleven B. rapa accessions were misclassified in genebanks as oilseed types but were re-classified as leafy or root vegetable types, and 12 accessions were misclassified as B. rapa and were shown to be allotetraploid or other Brassica species.