The anatomy of three endemic species in Türkiye, previously classified under the genus Pseudosempervivum (Brassicaceae), considered as the N. aucheri species complex (Noccaea aucheri, N. sempervivum and N. mummenhoffiana) in this study, was comprehensively evaluated anatomically for the first time. To aid the taxonomy of these three species, known for their transitional forms and classification challenges, 15 different populations were sampled, covering the entire distribution range of the species complex. The study investigated anatomical characteristics, such as root, stem and leaf anatomy, as well as stomatal index, which complement morphological identification traits, and examined their correlation with environmental factors. Root diameter and root cortex diameter, which are considered important for distinguishing perennials, showed the highest values in N. mummenhoffiana populations, while N. aucheri populations showed considerable variability. Multivariate analyses highlighted the importance of stomatal cavity size in basal leaves and the number of myrosine cells in explaining anatomical variation. Correlation analysis between climatic variables and anatomical traits revealed associations with stomata and epidermis cell sizes in cauline leaves with temperature and precipitation. Overall, the measurements indicated significant variability in anatomical traits among the three species within the complex, failing to provide clear distinctions. Alternatively, our results support the notion that the three species studied may represent a single polymorphic species.