The rice frog, Fejervarya multistriata, is an amphibian widely distributed in China. In this study, we sampled the species across its distributional area in China and sequenced the mtDNA D-loop to investigate the genetic diversity and geographical pattern of the frog population. The results revealed 38 haplotypes in the population, with K2P values varying from 0.19% to 4.22%. Both a phylogenetic analysis and a nested clade analysis (NCA) detected two geographically isolated lineages respectively distributed around the Yangtze drainage (Yangtze lineage) and the south of China (southern lineage). NCA inferred a contiguous range expansion within the Yangtze lineage and allopatric fragmentation within the southern lineage, which might be partly due to the limited samples from this lineage. Accordingly, Fu’s F_s test also indicated a population expansion after glacial movement. Therefore, we assumed that the species history responding to glacial events shaped the present population pattern of F. multistriata on the Chinese mainland.