Sunflower is one of the most important oilseed crops of world. Exploitation of heterosis has been very successful in cross pollinated crops and sunflower being cross pollinated is ideal for hybrid breeding. Exploitation of hybrid vigor with precision saves time and resources, and this can be achieved by using new genetic based crop improvement techniques like association mapping. Association mapping has proved very successful in designing molecular marker based speedy crop improvement. Agro-morphological traits are important for sunflower breeders in selection of genotypes with high performance and other yield contributing traits. Ten agro-morphological characters i.e., days to flower initiation and completion, plant height, stem curvature, head diameter, number of leaves per plant, leaf area, hundred seed weight, seed yield per plant and oil contents were used to study the genetic diversity in 109 sunflower lines at morphological level. A high genetic variability was observed among sunflower lines in field conditions. Population structure and linkage disequilibrium was estimated after genotyping through 40 SSR (simple sequence repeats) markers, that amplified a total of 65 DNA bands to locate the QTLs (quantitative trait loci) controlling the important yield contributing agro-morphological traits. Based on population structure analysis, sunflower genotypes showed two sub-populations. For identification of important QTL's controlling the morphological traits, genotypic and phenotypic data combination showed eleven SSR bands had a significant association (P < 0.05) with 6 out of 10 tested agro-morphological characters. These identified marker trait associations are expected to be helpful for sunflower breeders in designing a successful breeding strategy.