The seasonal and vertical abundances of ciliates and flagellates are described over a 2 yr period in Lake Kinneret, Israel, a warm meso-eutrophic monomictic lake. Ciliate numbers ranged from 3 to 47 cells ml(-1). At the thermocline and oxycline region, the highest ciliate numbers were observed in autumn, with Coleps hirtus as the dominant species. Maximum heterotrophic nanoflagellate abundance (1300 cells ml(-1)) was found in the epilimnion in winter spring, minimum numbers (66 cells ml(-1)) occurred in autumn. Bacteria ranged from 10(5) to 3.10(7) cells ml(-1) with highest numbers at the decline of the Peridinium gatunense bloom and the lowest during winter. Protozoa, especially ciliates, appeared to be important food sources for metazooplankton. Top-down control is an important factor determining the structure of the microbial loop in Lake Kinneret.