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Archaeologists measure features in archaeological seeds primarily to document domestication during the Neolithic period. These same methods are less frequently used to study morphological changes associated with cultural selection of landraces later in time. For example, researchers have documented domesticated forms of chenopods during the Formative period in the Andes, yet there remains very little research on postliminary chenopod morphology. In this study, I use techniques developed to understand domestication, including scanning electron microscopy, to analyse charred archaeological Chenopodium spp. seeds recovered from the site Ayawiri located near Puno, Peru and dated to the Late Intermediate period (ad 1100-1450), almost 4,000years after incipient domestication of quinoa (Chenopodium quinoa). I found that this assemblage of chenopod seeds does not morphologically conform to modern varieties. Rather, these seeds are smaller than their modern counterparts. These findings indicate there was appreciable cultural selection of larger chenopod seed stock over the last 550years.