Island is a special kind of fence for rodent populations on islands. Island rodents may face increased risk of inbreeding and population decline due to isolation among islands and mainland. We investigated the population genetics of Chinese white-bellied rat (Niviventer confucianus) populations on 13 islands in the Thousand Island Lake region in 2008. These islands included 8 small (Chawuling S Island, CS; Zhongdao Island, ZD; Dengta Island, DT; Wushi S Island, WS; Qiaowuping Island, Q; Chawuling F Island, CF; Lanwang Island, LW; Zhusiwu Island, Z) and 5 large islands (Jieshou Island, JS; Dafanlong Island, D; Gaoxiange Island, G; Wushi T Island, WT; Dongmen Island, DM). Of them, JS was the largest one. One hundred ninety two individuals were captured, and the muscle samples were used to extract the genomic DNA. Thirteen microsatellite markers were selected to analyze the population genetics. Five to ten microsatellite loci deviated from Hardy-Weinberg equilibrium (HWE) significantly in the four populations on the small islands (DT, Q, CF, Z), but no significant deviations from HWE were found at any locus on the large islands. Our results showed that the mean numbers of observed alleles (Na) and effective alleles (Ne) were 7.385 and 5.952, respectively. Mean expected heterozygosity (He) and observed heterozygosity (Ho) were 0.819 and 0.930, respectively. Mean polymorphic information content (PIC) was 0.760, and mean Shannon's Information index (I) was 1.780. Based on these results, we concluded that the white-bellied rat populations on 13 islands had a high genetic diversity. The F-statistic (Fst) value of the 13 populations was 0.053; thus, mild genetic differentiation was found among these populations. Additionally, the Fst values among 3 populations on larger islands (G, WT and DM) were less than 0.05, and we considered that there was little genetic differentiation among the populations on 3 larger islands. However, the genetic differentiation of white-bellied rat populations between smaller and larger islands was conspicuous. We also detected relationships between genetic diversity and island area. Significantly positive correlations were found between PIC and island area (P = 0.023), as well as between I and island area (P = 0.009). Therefore, rat populations on the larger islands had higher genetic diversity, but relatively lower genetic diversity on the smaller islands. Furthermore, the level of genetic differentiation between populations on the small and large islands presented some difference to some extent. We considered that the reduction of habitat area might result in not only variation in genetic component during the evolutionary process, but also the rapid evolution of animal populations. That is, rodent populations with different habitat areas might face different survival pressures. For instance, populations on small islands might be subjected to increased mortality and high turnover of individuals, and thus experienced more variation in genetics during a short period than those on large islands. Evolution is generally thought to happen in a long-term process. However, this is not always the case, environmental factors, such as extreme temperature, environmental pollution, and so on, might accelerate the evolution of animal populations. On the islands, habitat area is an important factor influencing animal's survival, and rapid evolution might take place in the populations with smaller habitat area.