We analyzed bacterial communities of six distinct gut sites (the food bolus and mucus layer of the proximal small intestine, cecum and distal large intestine), using wild folivorous flying squirrels. We found significant spatial heterogeneity in composition, diversity, and species abundance distributions (SADs) of gut microbiota, corresponding to physicochemical conditions. High diversity was detected in the mucus layer of small intestine and the food bolus of cecum, followed by the food bolus of large intestine and the mucus layer of cecum, and relatively low diversity in the food bolus of small intestine and the mucus layer of large intestine, likely due to disturbance and resource partitioning. The SADs showed succession-like patterns in the food bolus communities from the proximal to distal gut. Notably, each mucus layer community had a unique pattern different from the food bolus community of the same compartment, with distinct relative abundances of dominant species. In combination with data from other mammalian fecal samples, we concluded that gut microbiota were apparently dynamic in community structure, from low species richness with unequal abundances to high species richness with equal abundances; these findings were interpreted as strong habitat effects on bacterial communities.