Microbiota corresponds to the microbial associates that exist in the human body, and the genes they encode, the microbiome. Recent advances in genetic techniques are contributing to a better microbiota characterization. Imbalance in the intestinal microbiota - dysbiosis - is associated with several pathologies and reveals its important role as immunomodulator. These developments are particularly significant in ocular immunology, revealing physiopathologic mechanisms and identifying potential therapeutic targets.