Cultivated sunflower (Helianthus annuus L.) is an internationally important crop harvested for seed oil and confectionary purposes. Sunflower unlike many other crops, has an extensive root system that can provide drought avoidance under water limiting conditions in the field. This genome wide association (GWA) study utilized 2D images of seeds and seedling roots from a diverse panel of sunflower genotypes (n = 288 lines) for QTL detection. The subsequent analyses of these images revealed vast phenotypic variation in total root length (mean = 169 cm, SD = 81 cm) and primary root length (mean = 29 cm, SD = 7 cm). ANOVA and PCA based on population information assigned by STRUCTURE indicated significant differences between restorer lines and maintainer lines for both seedling root and seed traits. In total, 29 unique markers associated with seed size and shape and seedling root traits were identified. This study provides the groundwork for future experiments with the final goal of identifying markers that breeders can use for marker assisted selection to improve sunflower seedling emergence and establishment.