Our aim was to obtain details of the condition of the scimitar-horned oryx (Oryx dammah) and to elucidate the gut microbial diversity of captive individuals of this species. For the first time, 16S rRNA barcoding was used to characterise the faecal microbiota of five captive scimitar-horned oryx individuals. A total of 15 prokaryotic phyla were identified in the five samples. Including Firmicutes (53.40-72.01 %), Bacteroidetes (12.94-23.72 %) and Proteobacteria (1.03-31.74 %), accounting for > 96 % of all the sequences. At the family level, there were < 3.5 % unclassified sequences. In conclusion, these data revealed similarities and differences in gut microbial diversity across the scimitar-horned oryx individuals. These observations advance the current understanding of the bacterial ecosystems in these endangered animals under captivity.