The collective genomes of the different microbes (bacteria, fungi, protozoa, yeasts, archaea and bacteriophages) that live inside the horse hindgut compose its intestinal microbiome. This microbiome can be characterized by its microbial community structure (diversity and composition) and function (metabolic activities and resulting end products). It plays a vital role due to its capacity of hydrolysing and fermenting cell-walls into volatile fatty acid that represent an essential energy source for the host. Although not fully understood, it also completes important roles in health and several diseases pathophysiology. Traditionally, the microbes of the horse hindgut were studied using culture dependent techniques. More recently culture-independent methods have been used and have brought new insights. Regarding the ciliate protozoa community, 18S rRNA gene pyrosequencing allowed identifying 15 genera in the feces of pasture-fed horses. Most of these genera had been identified in previous microscopy studies. The 2 clades Methanobrevibacter ruminantium and Methanocorpusculum and their relatives were showed to dominate the fecal Archaea community using 16S rRNA gene pyrosequencing as it had been reported via cultural techniques. Regarding the bacteria community several studies have been done with molecular methods such as fingerprint techniques or more recently 16S rRNA gene pyrosequencing. In the cecum and colon, Firmicutes and Bacteroidetes are the 2 predominant phyla. Firmicutes comprise Clostridium spp., Ruminococcus spp., Butyrivibrio spp., and Eubacteria spp. that play a major role in fiber degradation. The cellulolytic species Fibrobacter succinogenes was identified recently as the second most abundant species in the horse feces. Although a phylogenetic core bacteria community appeared to exist in all regions of the large intestine of healthy horses, strong inter-horse variations on bacteria populations are often reported. The microbiome can also be affected by several factors. The effect of the diet has been the most extensively studied on the microbial community structure and function. Understanding the microbiome changes and the factors in cause can help manipulating the microbiome to improve nutrition and health.