Four exotic high oleic acid safflower germplasm and five conventional high linoleic acid varieties were taken for crossing in this investigation. Nine F2:3progenies of the crosses were screened for fatty acid profile. The fatty acid C18:1 recorded retention time of 18.20 minutes where as C18:2 recorded the retention time of 19.17 minute. Among the five crosses of F3 progenies EC-755669 x GMU-370878.06), SSF-748 x EC-755659 (47.11), Nari-57 x EC-755681 (40.37) and Nari-57 x EC-755669 (39.89) mg/g of oleic acid showing improvement in oleic acid content. The amplification of genomic DNA of F3 progenies of EC-755669 x EC-523373 and EC-755669 x GMU-3708 crosses with three SCAR primers linked with high oleic acid trait showed expected amplicon of 365, 730 and 150 bp with CAR FAD2–1, IASCA-73, IASCA-74 primers. The high linoleic acid parents SSF708, Nari-57, GMU-3708, SAF-1244 and SSF-748 also exhibited an expected amplification band when amplified with high linolate specific SCAR primer. The cross transferability with ORS-371 (550bp), ORS-488 (180 bp) and N1–3F (280bp) SSR primer which are previously used in high and low oleate sunflower genotypes is confirmed in our study with expected amplicon in F3 EC-755669 x EC-533373 and EC-755669 x GMU-3708.