De novo sequencing of complex eukaryote genomes by a Next Generation Sequencing (NGS) shotgun approach is fast and cost-efficient, but the short read length and the short insert libraries used, only allow the production of highly fragmented assemblies. The duck genome, for example, was sequenced at 65X coverage using exclusively the IlluminaTM Genome Analyzer technology and assembled into scaffolds, for which the N50 contig was 26kb and the N50 scaffold 1.2 Mb. To organize the scaffolds into chromosomes, we sequenced 100 hybrid clones from a duck radiation hybrid panel recently developed in our laboratory with a Hiseq 2000 platform. The nearly 1 billion pair-end reads were first aligned to the mouse genome to filter out hamster sequences. The reads were subsequently aligned to the duck scaffolds to identify duck specific reads. In this RH mapping experiment, the scaffolds are regarded as markers and their presence or absence determined by the aligned reads. More precisely; scaffolds with a significant number of reads were called present in the hybrids and those with unexpectedly low number or with no reads absent. As a primary result, a set of 1349 scaffolds were organized in 30 linkage groups spanning 841 Mb. Alignment of these scaffolds to the chicken genome revealed an almost exact correspondence between linkage groups and chicken chromosomes, as suggested by previous FISH experiments, confirming the validity of our approach. Refinement of the RH maps will allow characterizing evolutionary rearrangements between duck and chicken.