Anurans are the most suitable vertebrate group to see the development and also evolution in the skull, compared to other terrestrial vertebrates as they show highly derived morphology. For this reason, the cranium of anurans has been widely used for analyzing e.g., development and integration, evolutionary history, phylogenetic relationships, sexual dimorphism; and for taxon determination. We applied geometric morphometric techniques and then multivariate statistical analyses to see the skull size and shape variations in closely related Bufo species (B. bufo and B. verrucosissimus) inhabiting Turkey. Females have larger skull than males for both species. Ventral skull size of males differed between species and within species (among populations) whereas dorsal skulls differed only among populations. In females, only size of ventral skull side differs only among populations. Dorsal skull shape differs between the species in male individuals, while in females both dorsal and ventral skulls show a significant variation among populations. Bufo bufo had larger squamousal than B. verrucosissimus, whereas B. verrucosissimus had longer maxilla but shorter occipital region than B. bufo for both males and females. Under the control of size, the shape of skull does not differ between species for both males and females. Due to structural and functional constraints because of having similar biological and physical properties of skeletal and muscle tissues, living in similar environments or shared evolutionary history, the size and shape of skulls are found to be similar between B. bufo and B. verrucosissimus in present study. However, in order to better reveal the skull variations between these two closely related species, more detailed studies with more samples on their morphology and ecology are required.