High density genetic maps can provide a framework to address many of the questions of genetics and plant breeding. We produced multiple high density genetic maps of sunflower Helianthus annuus by two different high throughput technologies. A 9,480 gene Illumina chip was used to create genetic maps from 4 different sunflower crosses with 3500 to 5500 loci each. These 4 maps were combined and integrated with a previous SSR map of 1512 loci to produce a sunflower map of 10,080 loci. Additionally genetic maps were constructed with the same Illumina chip on two related sunflower species. A 2.3 million feature Affymetrix chip was also used to map a single sunflower cross, with 130,707 features being mapped, corresponding to over 20,000 genes. If we combine the Illumina and Affymetrix maps we have mapped over 25,000 genes. Genetic mapping of multiple crosses made it possible to resolve genetic regions which showed reduced recombination in one cross, and to map regions that appeared identical by descent between the parents in some crosses. The maps are being used for whole genome assembly, association mapping, and QTL mapping.