Morphological and karyotypic characteristics have been used to classify A. cepa (bulb onion), A. fistulosum (Japanese bunching onion), and at least six wild species into section Cepa. Maternal phytogenies were estimated by restriction fragment length polymorphisms (RFLPs) in the chloroplast DNA. Allium oschaninii appeared most closely related to the progenitor of all species in section Cepa. A well supported maternal clade containing A. altaicum A. cepa, A. fistulosum, A. galanthum, and A. vavilovii was present in 100% of the bootstrapped Wagner trees. Random nuclear RFLPs revealed considerable divergence among species within this clade. Three distinct groups were identified, comprised of A. altaicum and A. fistulosum, A. galanthum, and A. cepa and A. vavilovii. Random nuclear RFLPs were then used to estimate relationships among open-pollinated populations of the bulb onion. Parsimony analyses suggested that long-day storage and short-day populations do not represent distinct sources of germplasm, but that long-day storage populations are a derived group selected for production at higher latitudes. Assuming that the sampled populations are representative, the collection and maintenance of short-day populations is important for the preservation of genetic diversity in onion.