Among the multifaceted environmental factors, the bacterial community ingested with soil and food might play an important role in physiological processes of terrestrial gastropods, with consequences on population dynamics and species distribution patterns. Therefore, we investigated the bacterial gut community structure and seasonal dynamic in three populations of the protected endangered land snail Helix pomatia. The PCR-DGGE fingerprinting analysis followed by Nonmetric Multidimensional Scaling (NMDS) showed that Gamma-and Alphaproteobacteria were common to all populations, while Mollicutes and Betaproteobacteria were population specific. Allochthonous strains might be transiently abundant in the gut of foraging snails with respect to habitat conditions. Autochthonous strains were permanently present in the gut, even after expulsion of the gut content at hibernation beginning. Some of these permanent strains are known to have ice-nucleating activity, which is consistent with the limited cold hardiness in this species. Snails that did not enter hibernation despite being exposed to winter conditions had a poor bacterial community. In conclusion, the bacterial community structure differed between habitats and physiological states, and might be important for physiological processes and survival. Further studies should focus on the individual variation in bacterial community and investigate how it is affected by environmental changes.