The view of relative importance of the roles of N and P concentrations, and the effects of 'bottom-up' and 'top-down' in regulating the spatio-temporal dynamics of rotifer community structure has been debated. In order to investigate their relative importance in controlling rotifer community structure in subtropical shallow lakes, the rotifers in two subtropical lakes, Lake Jiuliantang and Lake Tingtang located in Wuhu city, Anhui Province, were collected twice monthly from July 2011 to June 2012, and the relationships between the species richness, species diversity as well as evenness index of rotifer community in each lake, and the concentrations of N and P, as well as the densities of potential predators of rotifers were analyzed, respectively. Carlson trophic state index of Lake Jiuliantang and Lake Tingtang was 60.77 and 62.21, respectively, and both lakes could be characterized as slightly eutrophic. In all the environmental factors, only the annual average concentrations of TN and NO₃^-, and the annual average densities of the rotifer Asplanchna, the Cyclopoidea and its nauplius were significantly different between the two lakes (P<0.05). A total of 48 rotifer species belonging to 15 families and 21 genera in Lake Jiuliantang, and 55 rotifer species belonging to 15 families and 24 genera in Lake Tingtang were identified, of which Synchaeta, Brachionus and Trichocerca accounted for the most proportion of the rotifer species numbers in both lakes. The dominant species in density contained 7 species and 4 species in Lake Jiuliantang and Lake Tingtang, respectively. In Lake Jiuliantang, the densities of Cyclopoidea and its nauplius were higher in July, August, early September, November 2011 and April 2012 than in the other months (P<0.05). In Lake Tingtang, the densities of Asplanchna were higher in July, August, September, November 2011 and May 2012 than in the other months (P<0.05). The analysis of Pearson moment correlation showed the P concentration was negatively correlated with both the species diversity index and evenness index of rotifer community in Lake Jiuliantang (P<0.05), while the N concentration was positively correlated with the species diversity index of rotifer community in Lake Tingtang (P<0.05). In addition, the mass ratio of TN:TP showed positive relations with species diversity index in both lakes (P<0.05). Canonical correspondence analysis (CCA) indicated that both lakes exhibited a high degree similarity in rotifer communities and could be clustered as 'type Ⅰ and Ⅱ' when the densities of potential predators of rotifers, such as Cyclopoidea and its nauplius, and Asplanchna, were respectively high. The other rotifer communities in both lakes were assembled together as 'type Ⅲ'. All these findings suggested that the parameter of TN:TP (mass ratio) could be more suitable than single factor of N or P for reflecting the effects of N and P on the species diversity dynamics of the rotifer community structure. The spatio-temporal dynamics of rotifer community structure depended mainly on the effect of 'top-down' when the density of potential predators of rotifers were high, and the effect of 'bottom-up' were the most important factor in regulating the rotifer community structure when few potential predators of rotifers occurred in both slightly eutrophic lakes.