Anaerobic gut fungi of the class Neocallimastigomycetes are of great importance for herbivorous animals. Their immediate colonization and mechanical breakdown of plant particles pave the way for highly efficient enzymatic fermentation of complex plant polysaccharides. Neocallimastigomycetes are found in a variety of herbivores, yet so far studies almost exclusively investigated domestic or captive animals. Here, the occurrence and diversity of Neocallimastigomycetes in two different populations of sympatric, wild African forest elephants and forest buffaloes were determined. In both hosts together, a total of 16 species-equivalent Operational Taxonomic Units (OTUs) (0.05 cut-off level) were generated. Buffaloes harboured four and elephants five anaerobic fungi genera or genus-equivalent taxa, respectively, with four genera occurring in both hosts. In elephants the majority of gut fungi group within a cluster of yet unknown Neocallimastigomycetes. Similarly, some anaerobic fungi found in buffaloes form a genus-equivalent cluster with likewise undescribed gut fungi. Sequences grouping in these two clusters could potentially qualify as representatives of new anaerobic fungi genera. Further, three sequences have not yet been encountered in any study and cannot be assigned to any genus or genus-equivalent Neocallimastigomycetes taxon. Whether these sequences also represent putative new lineages needs further investigation.