The possible introduction of genetically modified potato in the Andean region raises concerns about the unintentional introduction of transgenes into the native potato germplasm because it is perceived to convey negative impacts on biodiversity. We investigated this question by an ex-post analysis of existing landraces resulting from natural hybridization between an unknown landrace and the fertile commercial variety ‘Yungay’. This variety can be regarded as exotic because it was bred in part from the southern Chilean germplasm of Solanum tuberosum Group Chilotanum. We sampled the landrace germplasm of 1,771 leaf samples comprising more than 400 different landraces from three regions where ‘Yungay’ and landraces have coexisted for 15–25 years in the Peruvian Andes. Simple sequence repeat (SSR) markers were used to identify putative hybrids based on allele sharing with those of ‘Yungay’. The exclusion procedure was iterative, starting with the SSR markers with highest discriminating capacity based on allele frequency of the variety ‘Yungay’ in our large database of 688 landraces by 24 SSR makers. With only 12 of the 24 SSR markers assayed, all of the samples could be rejected as possible hybrids with ‘Yungay’ as a parent. This result demonstrates that the unintentional introduction of a transgene, not under farmers’ selection, from a widely grown transgenic variety over a long period of time is unlikely to happen at a detectable scale. Our finding reinforces the prominent role of farmers in the selection and maintenance of landraces which, unlike hybrids, have specific characteristics that farmers appreciate.