The study was carried out to determine the achene surface morphologies of 21 taxa in five sections (sect. Pseudoseridia, Cheirolepis, Microlophus, Rhizocalathium and Pteracantha) belonging to the genus Centaurea L. in Türkiye via SEM. The surface structures of the achenes of each taxon were described in detail, and a dendrogram showing the close relationships of the species was obtained by converting the determined micromorphological features into numerical data with the PRIMER7 programme. The findings show that achene surface morphologies are of great importance in determining the taxonomic relationships of taxa. The structure and length of the pappus also play a critical role among systematic characters and species boundaries. The seed surface morphologies do not support the previous sectional assignments of the genus Centaurea in previous research. Particularly, the seed surfaces of some subtaxa of C. kotschyi and C. drabifolia were found to be significantly different, indicating the need for a taxonomic arrangement at the species level. In addition, it was thought that different populations of the C. isaurica taxon were differentiated considerably in terms of achene morphology and this might be related to interspecific hybridization. Additionally, the pappus structures were plumose, barbellate and scabrous and they could be simple or double-rowed.