Two of six captive capybaras in a zoo had developed diarrhea and were given metronidazole to which they responded and the fecal appearance improved temporarily, however, both subsequently developed severe watery diarrhea and died. A large number of ciliates of the family Ophryoscolecidae, which parasitize the intestinal tract, were found in the fecal samples from three of the four surviving animals. These ciliates could not be detected in the two dead and one surviving capybara with a history of previous metronidazole administration. These results indicated that it might be necessary to consider the influence on the microflora including some key symbiotic ciliates and bacteria for digestion and absorption in the digestive system.