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Abstract Key message Appropriate silvicultural practices combined with the use of resistant Central European provenances can reduce the prevalence of larch canker caused by Lachnellula willkommii (R. Hartig) Dennis, a major disease affecting larch plantations in France. However, cascading translocations have resulted in frequent admixture in European larch (Larix decidua Mill.) and subsequent certification errors regarding the origin of plant material. Our study highlights the urgent need to improve the certification process of seed orchards. Context The recent history of European larch has been marked by translocations of plant stock within and beyond its native range. In order to increase stand resistance to larch canker disease, it is strongly recommended by French authorities to plant Central European provenances. However, a recent disease outbreak questioned the resistance of Central European provenances and the origin of the forest material used in these plantations. Aims Our goal was to assess the effects of cascading translocations and mixing between larch gene pools on genetic composition of plantations and on their vulnerability to the disease. Methods In the outbreak area, we checked the genetic origin of the trees and we estimated the percentage of Central European trees, disease prevalence and severity. Results Intra-site genetic diversity was high. Genetic composition did not match with geographic origin certificates. A high proportion of trees could not be assigned to either the Alpine or Central European gene pools. These admixed trees were as resistant as Central European trees. Geographic origin turned out to be one of the main drivers of canker prevalence, along with abiotic factors. Conclusion We need a precise knowledge of the origin of material used in seed orchards to mitigate canker disease and adapt forests through assisted migration.