Morphological analysis of plant remains from archaeological sites provides evidence regarding the domestication process of crop species, and the changing economic behaviors of humans during the foundation and intensification of agriculture. In contexts from the Neolithic and early state periods of Henan, China, morphometry of genus Setaria millet seeds is shown to provide data on production versus consumption contexts of archaeological deposits, in connection with site function and settlement hierarchy. Comparative morphometry of modern Setaria seeds sheds light on larger archaeobotanical issues, including problematizing the distinction between domesticated and wild/weedy seeds. Statistical analysis suggests that subdivision of archaeological millets below the genus level is less useful in some cases than consideration and comparison of genus-level populations.