The mouflon’s traditional classification as a grazer has recently been questioned, therefore new insight into the species’ feeding and digestion is needed. The presence and share of different ciliate genera in the rumen may contribute to an understanding of a species’ feeding physiology, therefore we analysed the composition of mouflon rumen ciliates and correlated their density with the percentage of different food types eaten by the animals. We found that the dominant ciliates were Entodinium spp., with a small proportion of Anoplodinium denticulatum, Eudiplodinium maggii, Epidinium ecaudatum caudatum and Dasytricha ruminantium. The main food types taken by the animals were deciduous tree leaves, grass and bramble. The density of ciliates from the Entodinium genus rose with an increase in deciduous leaves in the diet and fell with an increase of graminoids in the diet. The density of ciliates from the Anoplodinium and Eudiplodinium sub-genera increased with a rise in tree shoots and was reduced with a rise of deciduous leaves in the diet. These results confirm that the protozoal fauna vary with current food composition in intermediate feeders.