Less study was focused on the ecological community of littoral rotifers than on pelagic area worldwide. Moreover, rotifers were overlooked mostly due to the improper sampling methods and lack of experienced taxonomists for ecological researches, and the diversity and role of estuarine rotifers in ecological systems were underestimated severely. A long-term investigation of the littoral rotifer in a shallow mangrove swamp (MS) and a tidal creek (TC) of Qi'ao Island, the Pearl River estuary of southern China, revealed significant differences of the community structure at different sites and in different seasons. Ninety-four monogonont rotifers were detected in total. The average abundance of rotifer at MS (97.0 individuals/L) was lower than that at TC (140.8 individuals/L), but all average diversity indexes at MS were higher than those at TC. The main species at MS were Colurella sp.1, Encentrum marinum, Colurella adriatica, Synchaeta cf. kitina, Synchaeta sp., and Cephalodella cf. innersi, whereas they were Synchaeta cf. kitina and Brachionus angularis at TC. The rotifer community was correlated with the salinity and total nitrogen group most at MS, while temperature contributed most at TC. This study revealed higher diversity and abundance of littoral rotifers at the two close mangrove wetlands of Qi'ao Island compared to other studies. Different kinds of biotopes at the two sites displayed significant difference of the community structure, which was mainly due to the abundance of different main species present at the two sites. The peculiar environment of MS created an unusual rotifer community which had more marine species with higher abundance mostly in winter.