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The Danube Delta Biosphere Reserve encompasses a complex of aquatic ecosystems with a mosaic of structural and functional features that influence significantly the biological communities. Ciliata group plays an important role as part of the zooplankton communities being a key factor in nutrient cycling within the microbial loop. The microbial food web gained lately a wide recognition especially in eutrophic and hypertrophic systems (such as the Danube Delta) as circulation pathway of organic matter within the planktonic trophic networks and reintroduction of inorganic forms of nutrients in the water rendering them available again to primary producers. In 2013 an intensive study was carried out covering a seasonal sampling program (spring summer autumn) in four large deltaic lake complexes. This paper focuses on the characterization of ciliate community highlighting also the biotic and abiotic factors that control this community in the investigated lakes. A number of 30 genera and species were identified the highest diversity being reached in the marine part of the delta (23 in complex Rosu – Puiu and 20 in Matita – Merhei) and the lowest in the fluvial complex Sontea – Fortuna (7). The abundance varied in a large spatial and temporal range in all the four lake complexes: in Rosu – Puiu it fluctuated between 38 ind L 1 in summer and a minimum of 0.28 ind L 1 in Mândra in spring; in Gorgova Isac it varied between 27.60 ind L 1 in Gorgostel in October and 0.22 ind L 1 in Uzlina in July; in Matita – Merhei it fluctuated between 48 ind L 1 in Merheiul Mic in October and 0.30 ind L 1 in Matita in May while in Sontea Fortuna complex it ranged between 1.60 in Ligheanca and 0.24 in Lake No name both in summer. In terms of spatial distribution of Ciliata abundance the maximum averages were recorded in Rosu Puiu complex (7.61 ind L 1 ) and the minimum in Sontea Fortuna (0.81). Anova single factor analysis reveals no statistically significant differences in terms of abundance in the 4 lake complexes (p>0.05 Fcrit>F). The corelation of ciliate development according to the season has been tested with single factor ANOVA and revealed that seasons affected statistically significant this community (p