In this study, Taxonomic differences between Microtus guentheri and Microtus hartingi, which are similar in terms of external morphological features, were determined using linear morphometric, geometric morphometric, karyological and molecular analyses methods. Through classical morphometric (mean values) and geometric morphometric analyses of craniodental and mandible characters, influenced by various genetic, developmental, and functional processes, it was found that M. hartingi and M. guentheri exhibited notable differences in both mean linear measurements and shape. The Jackknife in classical morphometric analyses of samples, which underwent molecular and karyological species diagnoses, was higher than 88 % for each character. In geometric morphometric analyses, the Procrustes distance for shape follows the order Ventral < Dorsal < Mandible < M3<M2<M1. Based on cross-validation, the accurate classification rate is between 73 and 100 %. In both mean linear measurements and centroid size, M. hartingi specimens exhibited significantly larger mandibles and craniodentals compared to individuals of M. guentheri. According to PLS results, there was a significant relationship between the shape of M1, M2 and M3 and environmental variables, while the relationship between their size and environmental variables was not significant. However, neither the shape nor the size of the other parts had an sufficient relationship with environmental variables. Both species exhibited karyological similarity with a chromosome number of 2n = 54, but display polymorphism in chromosome arm number. There were differences in the C-banding of autosomal chromosomes and X chromosome. The classification of species in classical and geometric morphometric analyses, diverges from the outcomes of karyological and molecular assessments. In both species, the intraspecific genetic distance remained below 1.35 %. The cyt-b exhibits significant differentiation between the two species (K2P = 6.55 %). The divergence time for M. guentheri from the clade containing M. hartingi + M. qazvinensis + Microtus dogramacii was estimated to be 0.73 million years ago. Since no sample of Microtus elbeyli with karyological and cyt-b characteristics was found in the samples taken from the type locality, the taxonomic status of M. elbeyli remains unclear.