Rotifers are important group of zooplankton and acts as good indicators of the changes in water quality as they are strongly affected by environmental conditions and respond quickly to changes in water quality. The present paper reports on diversity and seasonal fluctuation of rotifers in three different freshwater bodies of Manipur during 2013-2015. The three freshwater bodies selected for the study viz. Thongjaolok stream (24°30” N latitude and 93°45” E longitude), Phubala Irrigation Canal (24°60” N latitude and 93°79” E longitude) and Yenapat lake (24°38” N latitude and 93°48” E longitude) of Bishnupur district Manipur. Relative abundance of the diversity of rotifer in the concerned freshwater bodies were taken into consideration. About 21 species of rotifers were recorded from 5 families where Euchlanis lyra were recorded for the first time from Manipur.