In order to determine the phenotypic associations of four morphologically similar species of Microtus occurring in Turkey, we applied landmark-based shape analysis. The skulls of Microtus anatolicus, M. dogramacii, M. guentheri and M. levis (= M. rossiaemeridionalis) were found to differ significantly in terms of both size and shape. M. guentheri had the biggest skull, while M. levis had the smallest. Sexual dimorphism was found in the shape of the skull in M. dogramacii and M. levis. The tympanic bulla area is enlarged in M. anatolicus compared to the other species. Mahalanobis distances (the distance between a point and the group mean, taking into account the within-group covariance-variance matrix) confirm the distinction of the arvalis group (M. levis) and socialis group (Microtus anatolicus, M. dogramacii, M. guentheri).