Seed morphology and disk diameter are agronomically most important traits for the confection sunflower. This paper reports the results of an analy sis of quantitative trait loci (QTLs) underlying 10 seed morphological traits including seed and kernel size, shape and stripe, and disk diameter in both F2 population and F2:3 families derived from an oilseed by confection cross. A linkage map containing 165 target region amplification polymorphism (TRAP) and 44 simple sequence repeat (SSR) markers was constructed from 120 F2 plants. This map contained 17 linkage groups and spanned a total genetic dis tance of 1784.3 cM. A total of 51 QTLs were detected and 32 of them were identified in both generations. Each QTL explained 5.1-29.3% of the pheno typic variation, suggesting these traits were controlled by multiple genes. Most of the QTLs were clustered in six chromosomal regions. Two of the three QTLs identified for disk diameter were also located in two of the six regions. Moreover, alleles from the confection line at these QTLs had positive effects on these traits. Both QTL congruence and correlation analysis revealed that different genetic bases are responsible for seed shape, stripe, and other confection traits. The information generated by this study will facilitate confection sun flower breeding.