Higher plants are ubiquitously colonized with fungal endophytes, which often lack readily detectable structures. This study examines the diverse endophyte population within a single line of micropropagated Bouteloua eriopoda (Torr.) Torr., using microscopy and comparison of internal spacer (ITS) gene sequences obtained from both plant and isolated fungal tissues. Sequences amplified from three ascomycete and one basidiomycete fungi isolated from a micropropagated line were compared to seven unique, ITS sequences amplified directly from the fungal-laden micropropagated plant tissue. Clone sequences were also compared to grass ITS sequences. Bayesian analysis placed four of the seven sequences in a tight grass clade. The remaining sequences were placed in a more diverse clade representing both cultured and uncultured endophytes. Results confirm a diverse, cryptic endophyte consortium is retained within this micropropagated plant line. The probability that similar complexity is common among higher plants implies a need to revise commonly held assumptions that aseptically propagated plants are axenic. Genes and natural products derived from such systems could be microbial in origin. Meanwhile, while the development of controlled systems in which to study single plant-fungal interactions presents significant technical challenges, the potential to uncover multi-species interactions that influence plant growth and development is high.