Colonization patterns corresponding to individual endophytic species were observed in asymptomatic leaves and culms of Juncus imbricatus var chamissonis, a perennial plant. The presence of the fungi within the host was demonstrated by light microscopy after the cleaning and staining of tissues. The main endophytic species, Pleospora aff togwotiensis, was found colonizing the substomatal chamber and growing intercellularly between mesophyll cells. In a second colonization pattern, an unknown fungus was restricted to a single host epidermal cell, showing similar characteristics to other fungal taxa observed on Juncus effusus var pacificus, Pseudotsuga menziessii and Fagus sylvatica. A third colonization pattern, where the mycelium is confined to the substomatal chamber, was also described.