Plankton samples collected (November, 2002 – October, 2004) from Waithou and Utra pats, two floodplain lakesin Manipur state of northeast India, revealed species rich zooplankton (121 species) with diverse nature of Rotifera (75 species).The individual pats exhibited rich species diversity (110 and 103 species) and high monthly richness (68±7 and 61±8 species)respectively with higher community similarities. Zooplankton formed important quantitative component (56.0±4.3 % and55.1±5.1 %) of net plankton of the two pats; Rotifera dominantly contributed to their abundance while Cladocera > Copepodawere sub-dominant groups. The richness and abundance showed significant variations between pats and between months andfollowed oscillating annual patterns in each pat except for peaks during winter. Zooplankton indicated higher species diversityand evenness, lower dominance, lack of quantitative importance of individual species, low densities and equitable abundance ofthe majority of species in both pats. The richness correlated inversely only with nitrate in Waithou pat and abundance positivelycorrelated with alkalinity only in Utra Pat. Canonical correspondence analysis (CCA) with abiotic factors explained 55.6 % and61.8% cumulative variance of zooplankton assemblages of Waithou and Utra pats respectively along axis 1 and 2.