RH maps have been repeatedly used to assist whole genome assemblies. In the most recent examples (cow, pig, sheep), the RH mapping approach took advantage of the high density SNP chips providing a large number of markers that can be efficiently genotyped on the panel. In the absence of such a resource in duck, we sequenced 100 hybrid clones of the duck RH panel enabling direct genotyping of the assembly scaffolds on the panel. The rationale is as follow: the presence/absence of a scaffold in a particular sequenced hybrid is attested by the presence/absence of reads mapping specifically to this scaffold. The detection of scaffolds exhibiting a chromosomal breakage resulting from the irradiation process revealed itself to be a critical issue of this genotyping by sequencing process. This process resulted in the construction of RH vectors for 2027 scaffolds, representing a total of about 1 Gb of sequences (95% of the current Duck genome assembly). The subsequent linkage analysis enabled the construction of RH maps and therefore to organize, ie order and orientate, the scaffolds into pseudomolecules associated to the corresponding duck chromosomes. The whole mapping process, from sequence-based genotyping to the construction of comparative maps, will be presented as well as few examples of intra-chromosomal rearrangements that have been identified by the comparison with the chicken, turkey and zebra finch genomes and subsequently confirmed by FISH.