Ciliated protist assemblages of the shallow soda lakes Bogoria and Nakuru in Kenya were studied weekly during the short rainy season in October and November 2008 to identify their taxonomic composition and possible interactions with abiotic and biotic factors. Overall, 22 ciliate morphotypes were detected. Cyclidium glaucoma was the most abundant, whereas Frontonia sp., Condylostoma sp. and Holophrya sp. dominated in terms of biovolume. Further, the assignment of ciliates to nutritional modes indicated that the abundance of bacterivorous ciliates was not related to bacterial abundance, most likely because of the very high bacterial food concentrations (83.0 × 106 cells mL−1 on average). The abundance of Frontonia sp. was positively correlated with chlorophyll a in Lake Bogoria, but not in Lake Nakuru. Morphometric measurements of Frontonia sp. indicated significant intraspecific differences in mean cell length, i.e. 116.1 ± 2.3 vs. 139.0 ± 2.7 µm in Lake Bogoria and Lake Nakuru, respectively. Sequences of the 18S SSU rRNA, however, turned out to be identical for individuals of the two lakes. Phylogenetic relationships of the subclass Peniculia based on the 18S rRNA genes revealed that Frontonia from these lakes rather clustered with Apofrontonia and Paramecium than with other Frontonia species, indicating that the genus Frontonia is paraphyletic. With the exception of C. glaucoma and Euplotes moebiusi, the ciliate taxa from the two lakes could be identified only down to the genus level. We assume that these taxa are still not yet described and thus highlight the unique character of these ecosystems and the need for more studies.