As a ruminant herbivore, the cape oryx from southern Africa has a digestive system that allows it to absorb and digest large amounts of plant material through microbial fermentation in the hindgut. So far, there has been no study of the gut microbiota of the cape oryx. Here, we provided the first description of the fecal bacterial populations of the cape oryx by using high-throughput Illumina sequencing technology. We analyzed 100,180 high-quality sequences of the 16S rRNA gene obtained from fecal samples from three cape oryx animals, one female and two males. At the 3% level in our research, we found 3959, 4553, and 3930 operational taxonomical units (OTUs). Additionally, the three samples have 754 OTUs in common, which comprised 19.59%, 16.55%, and 19.81% of the reads in C1, C2 and C3. We identified 18 prokaryotic phyla in these animals, but most of the gut flora belonged to three phyla: Firmicutes (42.81-55.29%), Bacteroidetes (21.26-27.82%), Proteobacteria (3.05%-7.14%), represented by Ruminococcaceae, Lachnospiraceae, Prevotellaceae, Porphyromonadaceae, Succinivibrionacea and Rikenellaceae families. The present work offers an initial phylogenetic baseline for further research on the intestinal ecosystem of these African animals. This work is of great significance for disease monitoring and protection of these animals.