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As part of the comprehensive monitoring of the state of the ecosystems of the Reserve Kologrivsky Les, studies of the Myodes glareolus Schreber population organization were conducted for eleven years (20122022). To compare the values of craniological signs of the control population, similar measurements were considered in rodents living on the territory of Minskoe forestry in the Kostroma Region (20212022). The paper provides data on the size and proportions of the skull of this species. Osteological indices characterizing the nutrition ecology of the studied populations and their craniometric appearance were calculated. The variability and correlation of 17 craniometric signs of Myodes glareolus was analyzed in order to diagnose the degree of optimality of conditions for the existence of this species populations, as well as to assess the state of the environment in complex biological monitoring programs. Data were obtained on the patterns of variability of metric and nonmetric features of the skull in a number of years, and the influence of the sex structure of the population, the dynamics of its population, weather and climatic factors on the determinism of craniological measurements was studied. Sexual dimorphism according to these parameters was expressed slightly. There was a positive correlation of signs in rodents living on the territory of the biosphere reserve as the most optimal habitat in comparison with the territory of Minskoe forestry in the Kostroma Region, where a negative correlation was predominantly revealed. A strong correlation was established between some craniometric features characterizing the specifics of nutrition, population density, average precipitation and average air temperature. In addition, weak correlations between the body weight of individuals and the dimensions of the skull were revealed. When studying the fluctuating asymmetry of non-metric features of the left and right sides of the upper and lower jaw, a low level of the FAnm coefficient was found in the studied populations. Dynamic changes in the level of fluctuating asymmetry of rodents were insignificant. A weak negative correlation of the fluctuating asymmetry and the values of the average precipitation during the study periods were established. No significant correlation was established for the other factors. The results of the presented comprehensive study of the craniometric features of Myodes glareolus on the territory of the Kostroma Region indicate a stable state of populations in the considered environmental conditions.