Sunflower is native to North America and is now grown around the world for edible oil, seed roasting, confectionary products and bird food. Genetic diversity in cultivated and wild germplasm is characterized for use with various breeding objectives. Molecular markers have been developed to facilitate sunflower breeding. This review was undertaken to discuss molecular markers, which have been validated in different genetic backgrounds for traits of economic interest in sunflower. Markers found to be linked to monogenic traits in mapping populations may be used to select plants with those traits; review of the literature identified markers available for several monogenic traits including resistance against pests and pathogens. Markers linked to Quantitative Trait Loci (QTL) for many disease resistance and economically important traits that have also been identified in specific populations and target environments are also reported here. These identified linked markers should be validated in different genetic backgrounds and environments to ensure widespread utility. Publicly available inbred lines carrying traits of interest and validated markers related to them are summarized in this review, which also highlights traits for which these resources are still lacking, possibly due to lack of funding despite the importance of this hybrid crop. Genomic sequence data is now available for sunflower, which must now be exploited to develop new SNP based markers linked to genes of interest to mine allelic diversity related to economically important traits, especially traits well studied in other organisms, such as seed oil content and resistance genes.