The section Mesocentron is part of the genus Centaurea and is represented in Türkiye by four taxa, two of which are endemic. The aim of this study was to contribute to the separation of morphologically similar taxa through achene micro and macromorphology. The achene morphology of the section Mesocentron was examined in detail via scanning electron microscopy (SEM) and stereo microscopy (STE). A total of 24 characters were utilized, comprising 19 for the achenes and five for the pappus. The findings demonstrated substantial variation in the achene surface ornamentation of the examined taxa, underscoring their critical role in elucidating taxonomic relationships. Additionally, the results suggest that the achene color, indumentum, length, perimeter, surface area, and the pappus length provide valuable diagnostic features for identifying Mesocentron taxa. The first examination of achene surface area and perimeter in the genus Centaurea, the first observation of ‘imbricate’ surface ornamentation in achenes in any Centaurea species, and the first micromorphological examination of three of the four taxa indicate the importance of this study.