Ciliates are a morphologically diverse group of protists inhabiting aquatic and terrestrial ecosystems. We studied the taxonomy and ecology of free-living ciliates from a freshwater marsh in Central Mexico during the period from 2012 to 2013 during both dry and rainy seasons. We found 30 ciliate species recorded for the first time from Atarasquillo marsh in Mexico, most of which are common species in freshwater ecosystems. The species richness was higher during the dry season than rainy season. Five trophic groups were observed: bacterivorous, bacteria-algae-heterotrophic flagellate consumers (BAF-consumers), omnivorous, predators, and mixotrophic species. The trophic group composition changed according to the season and the environmental conditions, e.g. vegetation and water level. Generally bacterivorous ciliates were more frequent during the rainy season, meanwhile the omnivorous during the dry season; thus, the feeding strategies in ciliates were different between both seasons. Due to the fact that Atarasquillo marsh is in a deterioration process, ciliate records could be used to assess water quality.