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Heliosperma includes about 20 taxa which are divided into alpestre, macranthum and pusillum clades based on nuclear and plastid data. Based on microstructural qualitative and quantitative seed characters of H. macranthum, H. alpestre and of nine Balkan species, we found that the species assigned to the pusillum clade are highly variable and differ from H. alpestre and H. pusillum subsp. pusillum. Two low elevation species (H. retzdorffianum and H. nikolicii) were clearly separated from the H. pusillum group, which includes alpine taxa. Newly described characters of the seeds, e.g. two hilum chambers, two rows in crest and black colour could be treated as characteristic for lowland endemics. Microstructural differences in seed character of Heliosperma species seems to be mainly driven by ecological factors resulting from the elevation gradients. Pollen is undifferentiated between species, its viability (stainability) is high, chromosome number is 2n = 26, which differs from the number reported so far (2n = 24).