Distyly is a floral polymorphism with long-styled flowers and short-styled flowers. Traditionally, floral traits in distylous species have been studied as a variable composed of several linear measurements. We proposed the use of a geometric morphometric approach to studying flower shape and entire flower design variation (including stigma-anther polymorphism) between morphs in Palicourea padifolia. The geometric morphometric approach allowed us to preserve the integrity of the floral form and to project the floral features on the same scale. Moreover, the visualization of a grid deformation allows us to describe shape differences between morphs as well as to estimate the variance-covariance matrix among floral traits. In this study, we demonstrated that flower shape and entire flower design differed between morphs. Intra- and inter-morph variations in the flower size were observed. The flower size has an effect on the anther position between morphs and among individuals. An association between flower shape and flower size was observed in both morphs. A pattern of floral features co-variation between the morphs was demonstrated in the species. In P. padifolia both morphs seemed to be internally coherent with respect to the developmental processes that produce flower shape variation. Changes in floral traits associated with flower size seemed to be more complex than those in the simple uniform expansion of the floral trait positions analogous between morphs. The observed pattern of co-variation of floral features between morphs suggested that flower base shape would be an additionally ancillary trait linked to the stigma-anther polymorphism in the species.