The hindgut microbiota of equines enables them to utilize forage/grazing based diets which contain a substantial proportion of lignocellulosic fibres. These fibres are a structural barrier that gut bacteria need to overcome when accessing plant nutrients, as well as being a challenging and structurally complex substrate that can be utilized. The limited dietary energy available from these ‘natural’ diets however means that many equines are supplemented with energy-dense concentrate feeds in order to fulfil their dietary energy requirements. Use of energy-dense concentrate feeds however can change the equine hindgut microbiome, and lead to the development of gut-mediated diseases (i.e. fermentative acidosis, laminitis, colic and stomach ulcers). There is therefore a clear need to optimize the utilization of lignocellulosic fibres in the equine hindgut in order to minimize the need for dietary supplementation. The most effective of the fibre-degrading gut microbes, anaerobic fungi (phylum Neocallimastigomycota), are known to be a normal member of the equine gut microbiota. Despite this however, they have been largely overlooked in equine gut microbiology studies to date. Research being conducted within the EU funded EQUIANFUN project will therefore establish baseline knowledge of the phylogeny, community structure, physiology and nutritional impact of anaerobic fungi in the equine hindgut. The insights gained will inform the development of novel strategies to promote indigenous anaerobic fungal communities in the equine hindgut, enabling optimization of the use of dietary forage as an energy source in equids. Reduction of the use of energy–dense diets and applying targeted nutritional strategies for optimizing microbial health may counteract processes in the gastrointestinal tract that have been associated with disease. Anaerobic fungi therefore offer the potential to enable significant advances to be made in the optimisation of the nutrition, health and welfare of all domesticated equids.