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Technological changes embedded in the processes of agrarian modernization have profoundly reshaped agricultural environments, practices, discourses and institutions worldwide. This article explores how social–ecological relations shift in agricultural practices following the introduction of modern seed varieties, including hybrid and genetically modified (GM) seeds and their co-technologies. Drawing on interviews and ethnographic work in smallholder maize farms in South Africa, we introduce the concept of ecological deskilling in agriculture and describe three dimensions related to it: loss of ecologically based practices, loss of relational knowledge, and loss of socio-ecological agency. Our findings suggest that the introduction of modern seed varieties may contribute to the process of ecological deskilling due to the disruption of the co-evolution of knowledge between smallholder farmers and agroecological environments. We argue that this form of deskilling can undermine food sovereignty and farmers' agency. It can also narrow future possibilities and pathways for sustainable agricultural development. [ABSTRACT FROM AUTHOR]