Archaeological studies of plant remains have indicated that an increase in seed size is frequently correlated with both intensive cultivation and domestication of seed crop plants. To test if starch granules of domesticated root crops are significantly larger than those of wild or less intensively cultivated plants, archaeological and modern specimens of manioc and sweet potato were sampled for starch granules, and granule size was compared across a temporal sequence. The results indicate that a gross generalization can be made that modern specimens of both manioc and sweet potato yield larger starch granules than some archaeological specimens. It does appear, however, that modern domesticated manioc roots produce significantly larger-sized starch granules than those of its purported wild ancestor. Additionally, there exist two lines of evidence that the coastal Peruvian and lowland Neotropical regional types of manioc differ from one another and have been separate for several millennia. These findings indicate that manioc may have been domesticated more than once.