Having evolved as a grazing animal, a horse’s digestive physiology is characterized by rapid gastric transit, a rapid but intense enzymatic digestion along the small intestine, and a long and intense microbial fermentation in the large intestine. The process of understanding and describing feed degradation mechanisms in the equine digestive system in general, and in the hindgut ecosystem in particular, is essential. Regardless of its importance for the nutritional status of the host, the significance of the cecum-colon ecosystem has not yet been fully understood, and few reports have focused deeply on the contribution of the hindgut microbial population to the nitrogen and energy requirements of the horse. Compared to ruminal activity, very little is known about hindgut ecosystem activity in the horse. Information concerning the metabolism of this microbial population and its requirements is lacking. The use of internal bacterial markers for quantifying microbial outflow in ruminants is widely reported. These techniques can be applied to cecum-colon microbial quantification, contributing to a better characterization of this ecosystem. It is likely wrong to believe that the optimization strategy in the hindgut is similar to what happens in the rumen – that is, to maximize microbial growth and, therefore, fermentation. If we consider the type of substrate that, in normal conditions, arrives in the hindgut, we can expect it to be nitrogen limiting, providing limited nitrogen-based substrates for microbial fermentation. In this review paper, we intend to gather existing information on the equine ecosystem and to provide future perspectives of research.