Historical results from provenance trials tended to position Sudetan larch (Larix decidua Mill. sudetica) populations among the least susceptible to larch canker (Lachnellula willkommi (R.Hartig) Dennis), in sharp contrast to Alpine populations. However, a recent large-scale outbreak of larch canker in artificial French stands planted with Sudetan larch brings into question this conclusion but also, as a consequence, the value of Sudetan larch seed orchards to mass-propagate risk-limited forest reproductive material. Clonal material from the French breeding population and seed orchards was investigated for its susceptibility to larch canker. As a first step, a genetic structure analysis of this population (220 clones) was conducted: it revealed its genetic heterogeneity, with 53.1% of the clones classified as “pure” Sudetan, 3.1% as Alpine; 1.5% as Central European and 42.3% as introgressed. Following artificial inoculation, “pure” Sudetan clones appeared generally less susceptible to canker than Alpine clones; admixed clones behaved in a similar way to the pure Sudetan material. However, the broad clonal variability observed within each population prevents the sole use of genetic origin of clones to rogue the most susceptible ones within orchards. Artificial inoculation is, so far, the only reliable way to properly assess clonal behaviour towards canker and thus support genetic roguing of orchards.