The Dongting Lake region is one of the areas prone to flood disaster in China. Despite the frequent occurrence of flooding in this area, few studies have analysed its effects on rodent communities, especially their recovery after withdrawal of floodwaters. We carried out a study of rodent recovery after flooding of the Dongting Lake region in 1998. Rodent population monitoring in the flooded countryside of the Dongting Lake region was conducted during 1998–2001. The census was conducted in Anzao polder of Anxian County in Hunan Province, where the dike burst in 1998 and thousands of hectares of farmland were flooded from July to October. The results indicate that flood disaster could provide important changes in rodent community structure. Firstly, species abundance in the post-flood area became less than in the normal area. Striped field mice Apodemus agrarius colonized the flooded area in farmland until March 2000, and Norway rats Rattus norvegicus and house mice Mus musculus occurred in July and December 2000, respectively. The degree of the effect on the rodent community in residential premises is less than that in farmland. However, the rodent community in the flooded area could recover and become similar to the normal community. The recovery of rodent species composition was faster in residential premises than in farmland after flooding. Secondly, there was a similar tendency of the dominant concentration indices between post-flood and normal areas. Thirdly, inundation for a long period could reduce the species diversity of the rodent community in farmland. The significant difference in abundance was continued to 2000 in post-flooded farmland; however, the influence on the rodent community in residential premises was less and their diversity indices did not differ in 1999. Similarity indices indicated that variation between post-flood and normal areas had been gradually becoming low from 1999 to 2001. Finally, the monitoring data showed that rodent populations in the flooded area were less than those in the normal area in the first step after withdrawal of floodwaters. However, the rodent population increased rapidly in the flooded area, and became greater than that in the unflooded area in half a year. The population in the flooded area also increased faster than that in unflooded neighbouring area after the application of rodenticide. Another phenomenon was that the population density of rodents could reach levels greater than the normal area, and may continue for more than 2 years. Flood disasters could reduce population densities and species abundance, species diversity and evenness, while increasing dominant concentration indices of the rodent community. However, after 3 years, the rodent community structure became similar to that in the non-flooded area, except for high density. The recovery of rodent communities in residential premises was faster than that in farmland for a lesser degree of flooding.