Chemical compounds in seeds exert negative and even lethal effects on seed-consuming animals. Tannin-degrading bacteria in the guts of small mammals have been associated with the ability to digest seeds high in tannins. At the population level, it is not known if tannins influence rodent species differently according to the composition of their gut microbiota. Here, we test the hypothesis that sympatric tree species with different tannins exert contrasting effects on population fluctuations of seed-eating rodents. We collected a 10-year dataset of seed crops and rodent population sizes and sequenced 16S rRNA of gut microbes. The abundance of Apodemus peninsulae was not correlated with seed crop of either high-tannin Quercus mongolica or low-tannin Corylus mandshurica, but positively correlated with their total seed crops. Abundance of Tamias sibiricus was negatively correlated with seed crop of Q. mongolica but positively correlated with C. mandshurica. Body masses of A. peninsulae and T. sibiricus decreased when given high-tannin food; however, only the survival of T. sibiricus was reduced. The abundance of microbial genus Lactobacillus exhibiting potential tannin-degrading activity was significantly higher in A. peninsulae than in T. sibiricus. Our results suggest that masting tree species with different tannin concentrations may differentially influence population fluctuations of seed predators hosting different gut microbial communities. Although the conclusion is based on just correlational analysis of a short time-series, seeds with different chemical composition may influence rodent populations differently. Future work should examine these questions further to understand the complex interactions among seeds, gut microbes, and animal populations.