Societal Impact Statement The problem of genetically modified maize contamination in Mexico is the result of both planned and unplanned consequences of scientific and political choices. We show how a risk management strategy based on the modernist dichotomy between “modern” and “native” has failed to protect Mexican landraces and has marginalized other forms of knowledge that are urgently needed to understand and support the fluidity of Mexican biocultural landscapes. Farmers' seed systems are a fundamental source of crop resilience and evolution. They can constitute safe pathways for creating new maize varieties able to withstand climate and societal changes. Summary In 2001, an alert on the contamination of Mexican maize landraces by genetically modified (GM) maize spurred new actions to conserve the world's biggest reservoir of maize genetic diversity. We analyze how the largest maize collection effort in Mexican history, and the definition of the conservation procedures employed in it, either involved or marginalized different approaches to this environmental problem. The article is grounded in the sociohistorical analysis of the controversy of GM maize contamination and brings together new historiographical perspectives on Mexican scientific and political interest in native maize. It also draws on ethnographic approaches, extended fieldwork, and analysis of data from Mexican government agencies. We show how different epistemological traditions have made the risk of GM maize contamination (in)visible and thereby generated normative choices. We illustrate how the GMO controversy brought the theme of native maize back onto the Mexican political and scientific agenda. The normativity that shaped the controversy in the 2000s influenced current knowledge and how the problem of GM maize introgression is still addressed today. The entanglements between biotechnology, native landraces, and farmers' practices are too dense to be “scientized” and kept separate to be made manageable as areas of purely technical “risk.” The result is a geography of maize infused with all sorts of temporalities and materiality, which escapes the bounds of technoscientific framings. This intricate environment‐making process calls for new collaborations among epistemic cultures to tackle the possible consequences of GMOs for agrobiodiversity, seed systems, and their resilience.