Obligate fungal endophytes form cryptic communities in vascular plants which can defy detection and isolation by conventional methods. Molecular detection by PCR amplification of fungal DNA sequences alone is insufficient, since target endophyte sequences are unknown and quite similar to 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 produce specific bands unique for each organism present in a specific plant-endophyte community. This method has successfully identified endophytes in B. eriopoda and A. canescens, and has tracked these endophytes as they are transferred to novel host plants. The detection and monitoring capabilities of DGGE make it a valuable tool for discovery, characterization, and monitoring of rangeland endophytes.