The polyploid species Herbertia lahue (Molina) Goldblatt is widespread in the grassland areas of southern America. In this study, genotypic and phenotypic variations among hexaploids and octoploids from H. lahue were assessed based on quantitative floral traits and ISSR markers. Additionally, gynoecium and breeding systems were analysed through anatomical analysis and hand-pollination experiments. Cytotypes are self-compatible, and the anatomy of the embryo sac remains similar in hexaploids and octoploids. AMOVA indicates that hexaploid populations are less genetically variable than octoploids (respectively 4 and 22 %, P \ 0.001), thus the largest source of genetic variation for H. lahue lies among populations (82 %, P \ 0.001), probably a combined effect of selfing, changes in population size, and local adaptation. Genetic variation between cytotypes was significant (16 %, P \ 0.001), though unclear segregation among cytotypes was discovered through PCoA. A Mantel test indicated no relationship between geographic and genetic distances (r = 0.04; P = 0.37), possibly as a result of the combined effect of the recurrent origin of polyploids, gene flow restricted by selfing, and poor capacity for seed dispersal. In terms of floral measurements, eight measures of perigonium, androecium, and gynoecium varied significantly between cytotypes, though no clear grouping was defined by PCA. Presumably, complex variation in floral characters across cytotypes may result in the absence of distinct grouping by PCA. The combined use of ISSR markers and morphological characters revealed a complex relationship between H. lahue cytotypes shaped by both intrinsic and extrinsic factors.