In order to explore the characteristics and key factors of zooplankton community of two national aquatic germplasm reserves in the middle reaches of Huaihe River, samples were collected in winter of 2014. Results indicated a total of 57 zooplankton species were identified in the two germplasm reserves.Among them, 38 species of zooplankton including 22 species of Protozoan(57.89%), 7 species of Rotifers(18.42%), 6 species of Copepods(15.79%) and 3 species of Cladocera(7.89%)were found in the Huainan germplasm reserve;as well as 39 species of zooplankton including 23 species of Protozoan(58.97%), 6 species of Rotifers(15.38%), 7 species of Copepods(17.95%) and 3 species of Cladocera(7.69%) were found in the Jingtuxia germplasm reserve.Protozoa were on predominance in the two germplasm reserves (22 and 23 species respectively) and the dominant groups are ciliates with shell of Protozoa.The average density of zooplankton in Huainan germplasm reserve was (1313.17±500.53) ind./L, and (1601.46±669.02)ind./L in Jingtuxia germplasm reserve, while the average biomass was (0.23±0.12)mg/L and (0.41±0.50)mg/L respectively.According to the standard of diversity index evaluation, the two germplasm reserves were moderately polluted and the water quality in Jingtuxia germplasm reserve was better than that in Huainan germplasm reserve.The result of Redundancy Analysis(RDA) shows that Depth, Tur, pH and SD were the main factors which affected the zooplankton community structure of Huainan germplasm reserve. Simultaneously, T, TP, PO₄^3--P,Chl.a, and COD_Mn were proved to be the main driving factors which influenced the zooplankton community structure of Jingtuxia germplasm reserve.