Association mapping is a reliable tool to detect the association between phenotypic and genotypic data through linkage disequilibrium. In the present study, 21 SSR and 19 TRAP markers were applied to investigate the genetic structure and association analysis in 53 Iranian sunflower parental lines, including 23 restorer and 30 cytoplasmic male sterility lines. In the phenotypic analysis, 18 morpho-physiological traits were measured. The population structure analysis identified two and five actual subpopulations (optimum K) across SSR and TRAP markers, respectively. Using SSR data, population differentiation measurements (FST) between the subpopulations ranged from 0.24 to 0.43 (average 0.32); using TRAP data, FST varied between 0.23 and 0.24 (average 0.24). Association mapping analysis indicated that SSR and TRAP markers were associated with 11 and 17 traits, respectively. SSR loci Ha 494-ar, Ha 806-ar, Ha 991-ar, Ha 1167-ar, Ha 1287-ar, ORS-53, and ORS-54 were associated with seed yield per plant, oil yield per plant, seed yield, and oil yield respectively. On the other hand, several TRAP markers, including K11F05/TRAP03, K11F05/TRAP03, and F15O11F1/TRAP03 were associated with flowering duration, maturity, and 1000-seed weight, respectively. In conclusion, the genetic structure and marker-trait associations reported here can be exploited for marker-assisted selection (MAS) in sunflower breeding programs. تفاصيل المقالة