Introduction Seed morphology is widely used as an auxiliary source of evidence in orchid systematics, but its taxonomic value varies among lineages. For several genera within Vandeae, the extent to which seed traits reflect phylogenetic relationships or provide diagnostic features remains insufficiently evaluated.Methods To assess the systematic relevance of seed characters, we examined a broad set of qualitative and quantitative traits across representatives of the genus Polystachya, including seed length, shape, and surface architecture. Measurements were obtained from scanning electron microscopy, and patterns of variation were compared within and among taxa to identify traits with potential diagnostic utility.Results The analyses revealed that some seed characters display consistent patterns within Polystachya, while others show overlapping ranges that limit their diagnostic value. In several cases, seed length and anticlinal wall features proved informative for distinguishing certain species, whereas surface ornamentation was more variable. No single character was universally reliable, but combined trait assessment increased discriminatory power.Discussion The results demonstrate that seed morphology provides a useful, though not standalone, source of taxonomic information within the studied group. Patterns observed across taxa indicate that seed traits can reinforce existing hypotheses of relationships and highlight potential discrepancies where boundaries may require reassessment. The findings emphasize the value of integrating seed morphology with molecular and ecological evidence to improve the resolution of taxonomic questions in Polystachya.