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noxia, and ciliates might play a very important role in the plankton community budget there. We analysed changes in the composition and biomass of the ciliate assemblage and other microbial loop components throughout the oxycline just at the end of stratification in a warm-monomictic lake, Lake Alchichica, Mexico (four samplings: 2006-2008, 2010); the results were compared with those obtained from another lake from the region, La Preciosa, sampled in 2010. Bacteria, autotrophic picoplankton (APP) and flagellates were analysed using epifluorescence microscopy. Ciliates were evaluated either in DAPI stained samples (looking for pigmented organelles and/or ingested phototrophs) or in quantitative protargol stain (QPS) permanent preparations, where they were identified at the genus or species level. The end of the stratification period in Lake Alchichica was characterized by almost uniform heterotrophic picoplankton (HPP) numbers (106 cells mL-1) throughout the water column. Meanwhile, APP showed epilimnetic and/or metalimnetic maxima of 105 cells mL-1 followed by an order of magnitude drop in the hypolimnion. A very important peak (105 cells mL-1) of the autotrophic or mixotrophic flagellate Pyramimonas sp. was observed repeatedly above and within the oxycline of Lake Alchichica. Ciliate biomass maxima were found around the oxycline and in the above-bottom layer. The top of the oxycline was dominated by Euplotes spp. and Spirostomum teres fine- to coarse-filter feeders (feeding upon APP, nanodiatoms and algae). Raptorial haptorids (in particular, Phialina sp.) were the second most important group, generally occupying the layer below euplotids, followed by Holophrya and Prorodon facultative anaerobic prostomes. Sometimes, strictly anaerobic Caenomorpha sp. was found to be important in the anoxic hypolimnion. Minute picoplankton feeding species (both APP and heterotrophic bacteria feeders) were important throughout the water column: in the epilimnion, vorticellids (2006-2008) or scuticociliates (2010) dominated. Typically, the scuticociliate maximum was located in the oxycline and/or above the bottom. Some microaerophilic species were isolated; thus, their identification could be carried out. However, the apparent polymorphic ciliate life cycles were not described completely, and the species composition was only estimated: two dominant species (SC 1 – Cristigera-like and SC 2 – Cyclidim-like) covered nearly the total scuticociliate biomass. Strictly anaerobic scuticociliates were not isolated but observed in the deepest layers of the lake (bacteria symbiotic Isocyclidium globosum and Cristigera sp.). Significant statistical relation within the ciliate distribution and environmental variables was not confirmed due to unique species composition in the respective years. However, general trends in the distribution of ciliates on a species level were observed. Scuticociliates, including two important tentatively identified species, did not present unambiguous ecological position, and the study of their live cycle should be the next step in investigations.