The distribution of the ciliate assemblage was surveyed along a depth gradient in the maar crater, athalassohaline, warm monomictic Lake Alchichica (Puebla, Mexico) from June 2003 to October 2006 (monthly). DAPI staining was employed to count ciliates while the Guantitative Protargol Staining was used for their identification. Peritrichs often numerically dominated the ciliate assemblage; a maximum of 54 cells ml(-1) (Rhabdostyla sp.) was observed in the surface layer at the end of the mixing period, during the development of diatoms (Cyclotella alchichicana), cyanobacterial (Nodularia sp.) bloom and its decay. Minute spirotrichs (particularly Halteria grandinella) and a haptorid, Belonophrya pelagica occasionally dominated the epilimnion while mixotrophic Euplotes cf. daidaleos and Pelagothrix sp. were important round the oxycline along with haptorids, particularly Phialina sp. Scuticociliates Cyclidium glaucoma, Uronema nigricans, and anaerobic ciliates Isocyclidium globosum and Caenomorpha sp. dominated within the hypolimnetic assemblages.