This study concerns the evaluation of leaf anatomical characteristics of the closely related genera Matricaria (4 taxa) and Tripleurospermum (14 endemic taxa, 15 accessions) in Turkey using cluster analysis (CA) and principal component analysis (PCA). All taxa have the same basic leaf structure composed of lower and upper epidermis including anomocytic or anomocytic-anisocytic stomata, parenchymatic mesophyll, and vascular bundle. Statistically significant differences based on ploidy level have been found without generic delimitation. The differences mainly concern stomatal length and the relative size of the vascular bundle. These anatomical characters can be used to distinguish diploid from polyploid taxa of the genera.