Allozyme surveys of cultivated plant species generally report little within-cultivar variation, but considerable among-cultivar variation. This trend contrasts with natural plant populations in which most allozyme variation resides within, rather than among, populations. The difference may be an artifact of the extreme inbreeding techniques used to develop and propagate these crops, rather than a consequence of domestication per se. To test this hypothesis, we compared the population genetic structure of 24 lines of radish cultivars — a domesticated species developed and maintained as open-pollinated, outcrossed populations — with four wild radish populations in California. Although the wild populations displayed more overall allozyme variation than the cultivars, most of the allozyme variation in the cultivars remains partitioned within, rather than among, lines. Apparently, how a crop is developed and maintained can have a profound influence on the organization of genetic variation of that species.