Species composition of the endobiotic ciliates from the faeces of zebras Equus quagga from different zoos was investigated. The tendency towards a decrease in the species diversity of endobionts in captivity has been demonstrated. Most species of endobiotic ciliates typical for zebras have not been found in animals kept in zoos; the number of species of bacterivorous ciliates – representatives of the family Buetschliidae – is often small. At the same time, zebras in captivity may have species of ciliates not found in a given host in natural habitats. The level of differences in SSU and ITS region sequences in geographical isolates of ciliates Cycloposthium edentatum, Cochliatoxum periachtum, and Tripalmaria dogieli was analyzed.