Nitrate respiration plays an important part in the global nitrogen cycle by initiating a chain of biologically mediated reductions of nitrogen oxides1,2. It involves the substitution of nitrate for oxygen as a terminal electron acceptor, occurs only in the absence of oxygen and is assumed to be performed only by prokaryotic organisms3,4. Here we present evidence for nitrate respiration in eukaryotes. Some Protozoa are known to be capable of living in anoxic water in lakes5,6; we show that in at least one genus of Protozoa (Loxodes) this capacity can be attributed to a dissimilatory nitrate reductase located within the inner mitochondrial membrane. The general acceptance of Loxodes as an extremely primitive protozoon7 strengthens the theory that nitrate-respiring bacteria are plausible ancestors of animal mitochondria8,9.