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  1. Maize (Zea mays ssp. mays) domestication began in southwestern Mexico ~9,000 calendar years before present (cal. BP) and humans dispersed this important grain to South America by at least 7000 cal. BP as a partial domesticate. South America served as a secondary improvement center where the domestication syndrome became fixed and new lineages emerged in parallel with similar processes in Mesoamerica. Later, Indigenous cultivators carried a second major wave of maize southward from Mesoamerica, but it is unclear whether the deeply divergent maize lineages underwent any subsequent gene flow between these regions. Here we report ancient maize genomes (2,300-1,900 cal. BP) from El Gigante rock-shelter, Honduras, that are closely related to ancient and modern maize from South America. Our findings suggest that genetic material from long-divergent South American maize was reintroduced to Central America. Direct radiocarbon dates and cob morphological data from the rock-shelter suggest that more productive maize varieties developed between 4,300 and 2,500 cal BP. We hypothesize that the hybridization of South and Central American maize may have been a source of genetic diversity and hybrid vigor as maize was becoming a staple grain in Central- and Meso- America.