We examined pollen grains and starch granules from a large number of modern populations of teosinte (wild Zea spp.), maize (Zea mays L.), and closely related grasses in the genus Tripsacum to assess their strengths and weaknesses in studying the origins and early dispersals of maize in its Mesoamerican cradle of origin. We report new diagnostic criteria and question the accuracy of others used previously by investigators to identify ancient maize where its wild ancestor, teosinte, is native. Pollen grains from teosinte overlap in size with those of maize to a much greater degree than previously reported, making the differentiation of wild and domesticated maize in palynological studies difficult. There is presently no valid method for separating maize and teosinte pollen on a morphological basis. Starch grain analysis, a recently developed tool of archaeobotany, appears to be of significant utility in distinguishing the seeds of teosinte from maize. We propose that the differences in starch grain morphology and size between wild and domesticated maize defined in this study may be associated with domestication genes in Zea that have been documented in the starch biosynthesis pathway. As previously reported, phytoliths effectively discriminate the female reproductive structures of Tripsacum, teosinte, and maize. Multiproxy microfossil studies of archaeological and paleoecological contexts appear to be effective tools for investigating the earliest stages of maize domestication and dispersals.