Ultra-high density genetic maps based on whole genome shotgun sequencing provide a useful scaffold for the assembly of large and highly repetitive plant genomes. We have constructed an ultra-high density genetic map for sunflower, which is the target on an ongoing sequencing effort. We sequenced Helianthus annuus cultivars RHA801 and RHA280, which are the parental lines of our core recombinant inbred line (RIL) mapping population, to an average depth of 10x. Alignment to the contiguous sequences of the draft sunflower genome assembly revealed over two million high quality SNPs fixed between the two parental cultivar lines. Ninety-six eighth generation RILs were sequenced to a mean depth of 1.0x. In the RILs, genomic regions were called as descended from one or the other parent based on the presence of at least ten SNP calls at informative sites. Perfectly correlated regions not exhibiting significant segregation distortion were binned for use as genetic markers. A genetic map of seventeen linkage groups corresponding to the seventeen H. annuus chromosomes was constructed de novo using a Minimum Spanning Tree algorithm as implemented in the MSTMap software. This map allowed us to confirm the composition of genomic scaffolds, assign them to linkage groups, and place them in linear order.