© 2020, © 2020 Botanical Society of Scotland and Taylor & Francis. Background: Maize in Mexico exhibits great genetic diversity, maintained by traditional practices of indigenous and non-indigenous communities, the same practices that have led to crop diversification over centuries. As one of the main staple crops worldwide, safeguarding the genetic diversity of maize is paramount to food security. Aims: This study evaluated the genetic diversity and population structure of traditionally cultured maize landraces in a rural seasonal agricultural community in Veracruz, Mexico, in order to learn how traditional practices shape these landraces, and propose strategies for their preservation. Methods: We analysed 118 individual maize samples belonging to five morphotypes (white, yellow, black, red and mottled) with eight microsatellite markers. Results: We encountered high genetic diversity, according to expected heterozygosity (He = 0.61). However, inbreeding coefficient and gene flow values suggested the existence of assortative mating, which causes low genetic differentiation. Population structure analysis identified three genetic pools, independent of grain colour. These findings suggest that all morphotypes belong to the same population, which is sub-structured due to assortative mating and gene flow related to local agronomic management. Conclusions: Current management practices in this community could lead to genetic erosion. In order to preserve diversity, wider regional seed exchange and selection for morphological diversity could be implemented.