Obligate fungal endophytes form cryptic communities in vascular plants which can defy detection and isolation by microscopic examination of reproductive structures. Molecular detection by PCR amplification of fungal DNA sequences alone is insufficient, since target endophyte sequences are unknown and difficult to distinguish from sequences already characterized as plant DNA. We have successfully separated fungal and plant ribosomal DNA sequences by amplifying plant-extracted DNA with polymerase chain reaction, and separating sequences with denaturing gradient gel electrophoresis (DGGE). The resulting electrophoregrams theoretically produce specific bands unique for each organism present in a plant-endophyte community. This method has successfully identified endophyte sequences in Bouteloua eriopoda and A.triplex canescens, and has tracked these endophytes as they are transferred to novel host hosts.