A comparison of published estimates of mycorrhizal and dark septate endophyte (DSE) colonisation from various ecosystems suggests that DSE may be as abundant as mycorrhizal fungi as judged by the proportion of host plants colonised in mixed plant communities, or by the extent of colonisation in sampled root systems. While many strides have been made in understanding the ecological significance of the mycorrhizal fungi, our knowledge about the role of DSE fungi is in its infancy. In order to provide a framework of testable hypotheses, we review and discuss the most likely functions of this poorly understood group of root-associated fungi. We propose that, like mycorrhizal symbioses, DSE-plant symbioses should be considered multifunctional and not limited to nutrient acquisition and resultant positive host growth responses. Admittedly, many mycorrhizal and endophyte functions, (e.g. stress tolerance, pathogen or herbivore deterrence) are likely to be mediated by improved nutritional status and increased fitness of the host. Accordingly, it is pivotal to establish whether or not the DSE fungi are involved in host nutrient acquisition, either from inorganic and readily soluble sources, or from organic and recalcitrant sources. Facilitation by DSE of the use of organic nitrogen, phosphorus and sulphur sources by plants is a topic that warrants further attention and research. Even in the absence of a clear nutrient uptake function, the extensive DSE colonisation that occurs is likely to pre-emptively or competitively deter pathogens by minimising the carbon available in host rhizosphere environment. The DSEs' high melanin levels and their potential production of secondary metabolites toxic or inhibitory to herbivores are also likely to be factors influencing host performance. Finally, the broad host ranges speculated for most DSE fungi thus far suggest that they are candidates for controlling plant community dynamics via differential host responses to colonisation. We emphasise the need for simple experiments that allow unravelling of the basic biological functions of DSE fungi when they colonise their hosts.