The genetic control of the synthesis of stearic acid (C18:0) and oleic acid (C18:1) in the seed oil of sunflower was studied through candidate-gene and QTL analysis. Two F(2) mapping populations were developed using the high C18:0 mutant CAS-3 crossed to either HA-89 (standard, high linoleic fatty acid profile), or HAOL-9 (high C18:1 version of HA-89). A stearoyl-ACP desaturase locus (SAD17A), and an oleoyl-PC de-saturase locus (OLD7) were found to cosegregate with the previously described Es1 and Ol genes controlling the high C18:0 and the high C18:1 traits, respectively. Using linkage maps constructed from AFLP and RFLP markers, these loci mapped to LG1 (SAD17A) and to LG14 (OLD7) and were found to underlie the major QTLs affecting the concentrations of C18:0 and C18:1, explaining around 80% and 56% of the phenotypic variance of these fatty acids, respectively. These QTLs pleiotropically affected the levels of other primary fatty acids in the seed storage lipids. A minor QTL affecting both C18:0 and C18:1 levels was identified on LG8 in the HAOL-9xCAS-3 F(2). This QTL showed a significant epistatic interaction for C18:1 with the QTL at the OLD7 locus, and was hypothesized to be a modifier of Ol. Two additional minor C18:0 QTLs were also detected on LG7 and LG3 in the HA-89xCAS-3 and the HAOL-9xCAS-3 F(2) populations, respectively. No association between a mapped FatB thioesterase locus and fatty acid concentration was found. These results provide strong support about the role of fatty acid desaturase genes in determining fatty acid composition in the seed oil of sunflower.