Annual species of sunflowers in the genus Helianthus vary greatly in their geographic distribution and evolutionary origin. Based on Bayesian clustering of nuclear markers spanning the whole genome, we found a clear distinction between H. debilis, H petiolaris and H. annuus individuals. However, structure often does not distinguish hierarchical sub-structuring and consequently, may only reveal the top level of population differentiation. Our study was not intended to resolve the phylogeny of Helianthus, as this would have needed much more extensive sampling. However, our results corroborate previous phylogenetic work that places H. praecox within H. debilis.