In this study, capsule and seed features were compared to determine diagnostic traits useful for differentiating taxonomy among 14 Polygala species native to Turkey. Capsule and seed morphology of the genus was examined using light and scanning electron microscopy. Principal component analysis, ANOVA, and Tukey tests were used to facilitate the elucidation of relationship between Polygala taxa based on quantitative characters. Capsule length, wing width, and elaiosome shape are taxonomically important morphological features differentiating species. Moreover, wing symmetry is sufficient to separate two groups in through examination of capsules. As per the results, the recently described the species, P. turcica, as morphologically distinct from other Polygala species. The elaiosome shape was most distinct in P. monspeliaca and P. vulgaris. Based on micromorphology, P. supina can be differentiated from other species by distinctive surface ornamentation. In contrast, seed shape and color are of low taxonomic value for distinguishing taxa studied herein. An identification key for the studied taxa is provided.