The rumen, a specialized foregut in herbivorous animals (Ruminantia), hosts microbiota of archaea, eubacteria, anaerobic fungi, and ciliated protozoa. Microscopic observations re-veal that the endosymbiotic ciliates account for about 50% of the total microbial mass in the rumen: up to 100 billions of ciliates may populate the rumen of a single cow. These ciliates play an important role in fibre digestion and the modulation of the fermentation pro-files. Classical (morphological) studies have identified more than 250 species of ciliates living in the various ruminants1,2. The number of species in an individual host is known to be highly variable, but the average number of species has been reported about 20 in cat-tle3, but less in sheep3 and goats4. However, as in all protists, the limited number of distinct morphological traits hampers an assessment of the ciliate diversity in the rumen. Molecular studies on rumen ciliates are rare, mainly due to difficulties in culturing these ciliates in vi-tro. Here we describe a molecular approach to study the phylogenetic diversity of rumen protozoa. The diversity of rumen protozoa was analysed by sequencing of 18S rDNA li-braries that have been created from PCR-amplified DNA of total rumen contents of cow, sheep, and a goat. These sequences were compared with the sequences of rumen ciliates obtained from GenBank and ERCULE. The phylogenetic analysis suggests that the ciliate population of the ruminal ecosystem can be much more diverse than previously assumed.