Phenotypic plasticity is the capacity of individuals to modify their phenotype in response to environmental changes. Fundamental to the way in which organisms cope with environmental variations, phenotypic plasticity is associated with all types of environmentally-induced variations, including changes to morphological, physiological, and behavioral processes. The skull morphology of mammals is the most important phenotypic trait, which changes during the evolutionary process. The Chevrier's field mouse, Apodemus chevrieri is a nocturnal and species endemic to China, and originated in the Palaearctic region. A. chevrieri is mainly distributed in the Hengduan Mountains and nearby regions of China, including Zhaotong, Kunming, Lijiang, Dali, and the land around the Lancang and Nu Rivers in Yunnan Province. A. chevrieri mainly inhabits farmland and its nearby shrubland, and is one of the main natural foci of plague in the Hengduan Mountains, which is a crossroads of species dispersal. The boreal species of the Palaearctic migrating southward, and tropical species from the Indochina Peninsula migrating northward, and thus is an area of interest for biologists studying mammal diversity. Meanwhile, the Hengduan Mountains are located in the west of the Yunnan Province, where there are many mountains and canyons. From west to east, there are dramatic changes in environmental conditions with changes in altitude, and noticeable changes were observed in the zone and non-zone landscape. In order to adapt to the different environments, animals inhabiting the area may exhibit different phenotypic variations, so A. chevrieri was employed as an ideal model for examining the relationships between phenotypic and ecological adaptations. The analysis of morphology is a fundamental part of many biological studies. With the development of more sophisticated statistical techniques, the sophistication of analyses of these types of data also increased. Since the 1980s, there was a fundamental change in the nature of the data gathered and analyzed, as scientists began to focus on the coordinates of landmarks and the geometric information relating to their relative positions. Geometric morphometrics, was hailed as a "revolution" in morphometrics. Morphological divergence among taxa was estimated quantitatively by analyzing the outline of the mandible. This method treats the mandible shape globally, and provides continuous data which can be used to compute phenotypic distances. In order to study the microevolution of species in the Yunnan province, with its special ecological environment, we applied geometric morphometric methods to the study of skull shape changes in different areas of A. chevrieri distribution, and used mitochondrial cytochrome b (Cyt b) gene and control region (D-loop) to investigate the gene type. The results showed that the Kunming and Hengduan Mountain populations (Zhongdian, Jianchuan, and Lijiang) exhibited obvious morphological and genetic variations. In particular, the dorsal and ventral of skull in A. chevrieri rarely overlap between the Hengduan Mountain populations and the Kunming population, with large variations between two populations having been noted. However, the side and lower side of the skull showed no significant variation between populations. Therefore, this study indicates that A. chevrieri in the Yunnan Province might be in the process of undergoing ecological speciation.