The community structures of rotifers and their seasonal variations in small lakes (Lake Nanhu and Lake Qianlong,) in an excavating coal subsidence region in Huaibei city have been investigated from March 2005 to February 2007. A total of fourteen species have been recorded, belonging to nine genera in Lake Nanhu, and twenty-seven species belonging to fifteen genera in Lake Qianlong. Average density of rotifers in Lake Qianlong (1916 ind./L) is about 10 times higher than that in Lake Nanhu (198.4 ind./L). Maximum density of rotifers is 6915 ind./L in Lake Qianlong and 1185 ind./L in Lake Nanhu. Rhinoglena frontalis is dominant species in winter and spring, while Polyarthra spp. and Trichocerca spp. are dominant species in summer and autumn. Among annual average density of rotifers in Lake Nanhu, Polyarthra dolichoptera, Trichocerca pusilla and Cephalodella catellina are 24.4%, 24.0% and 23.0%, respectively. Among annual average density of rotifers in Lake Qianlong, Trichocerca pusilla, Polyarthra dolichoptera and Anuraeopsis fissa are 31.5%, 27.2% and 7.3%, respectively. The ranges of Shannon-Wiener indices in Lake Nanhu and Lake Qianlong are 0 2.06 and 1.28 2.68, with average values of 0.67 and 1.99, respectively. The community structures of rotifers in the small lakes of an excavating coal subsidence region in Huaibei city are influenced by water temperature, nutrients and phytoplankton biomass.