Background: Compared to horses and ponies, donkeys have increased degradation of dietary fiber. The longer total mean retention time of feed in the donkey gut has been proposed to be the basis of this, because of the increased time available for feed to be acted upon by enzymes and the gut microbiota. However, differences in terms of microbial concentrations and/or community composition in the hindgut may also underpin this. Therefore, a study was conducted to determine the effect of equine type on the faecal microbiota of three types of domesticated equines: pony, donkey and pony × donkey hybrid (i.e. mule/hinny).Results: Equine type had no significant effect on faecal dry matter content or faecal concentrations of bacteria, archaea and anaerobic fungi. However, equine type did significantly affect the faecal community composition of prokaryotes and anaerobic fungi. Two bacterial genera were significantly higher in donkey compared to both pony and pony x donkey: Lachnoclostridium 10 and ‘probable genus 10’ from the Lachnospiraceae family. Equine type also significantly affected the anaerobic fungal community composition. Piromyces was significantly lower in donkey compared to pony × donkey, with pony not significantly differing from either equine type. In contrast, the uncultivated genus SK3 was only found in donkey (4 of the 8 animals), and not at all in pony or pony × donkey. Anaerobic fungal diversity, as indicated by the number of OTUs, was also significantly higher in donkey, with no significant differences found between pony and pony × donkey.Conclusions: Donkey faecal microbiota differed from that of both pony and pony × donkey. These differences related to an increase in the relative abundance and diversity of taxa with known, or speculated, roles in plant material degradation. These findings are consistent with the previously reported increased fiber degradation in donkeys compared to ponies, and suggests that the hindgut microbiota play a role as well as differences in total retention time of feed. This offers novel opportunities to generate more energy from dietary fiber, decreasing the need for energy dense feeds which are a risk factor for gut-mediated disease.