Ciliates are among the largest classes of protozoans. They can be found in almost every aquatic environment. Ciliates serve as an intermediate link in the energy transfer chain from picoplankton to zooplankton. They also serve as indicators of water eutrophication and pollution. Given the important roles that ciliates play in the ecology of aquatic ecosystems, their identification, morphological aspects, and taxonomic position are of great importance in order to conduct ecological studies. The present research aims to identify and study the plankton and periphyton ciliates of the Zayandeh Rud river and the reservoir. The identifications were done using the available keys and catalogs. As a result, 45 species from 30 genera and 19 families were identified in this study. There are nine families belonging to the suborder Gymnostomata, three families belonging to the suborder of Trichostomata, and seven families belonging to the suborder Hymenostomata. For the first time in this study, 45 new species of ciliates were reported in the study area and 25 new species in the country's aquatic ecosystems