Reproductive traits are important taxonomic characters in section Polygonum. However, the taxonomic value of this character remains uncertain because of morphological variability and overlap among taxa. The goal of this research was to evaluate the discriminatory power of a comparative analysis of the quantitative and qualitative morphological characters of the bracts, perianth, and fruit in selected representatives of sect. Polygonum. The sample included seven taxa from 54 populations inhabiting the Balkan Peninsula and the Pannonian and Wallachian plains, and 23 quantitative and 9 qualitative morphological characters were analyzed. The results revealed a high degree of similarity between certain taxa, particularly P. aviculare and P. arenastrum, as well as P. arenarium subsp. arenarium and P. arenarium subsp. pulchellum. Almost all qualitative characters, with the exception of pericarp ornamentation, were found to be unstable at the taxon level, calling into question their previously emphasized taxonomic significance. Although newly analyzed quantitative characters provided additional information, they did not enable complete separation of the investigated taxa. Overall, the results indicate that morphology alone has limited resolving power within sect. Polygonum and highlight the need for an integrative taxonomic approach combining morphological, molecular, and ecological data.