Differences in species composition, infection frequencies and fungal colonization were compared in asymptomatic leaves and culms of one annual and three perennial Juncus species in western Oregon. Stagonospora innumerosa was the principal fungus species isolated from culms of the annual, J. bufonius , and two of the perennial, J. effusus and J. patens , host species; Phaeosphaeria juncicola and Drechslera sp. were isolated from leaves of J. bolanderi . Characteristic mechanisms of penetration and colonization corresponding to individual endophyte species were observed in host tissue. Infections limited to a single host epidermal cell were characteristic of S. innumerosa, Drechslera sp. and an unidentified endophyte of J. bufonius . Infections by P. junicola originate in the substomatal cavity followed by limited intercellular colonization of the mesophyll. Cladosporium cladosporioides and Alternaria alternata were isolated at low frequencies from J. effusus, J. patens and J. bolanderi . Infections by C. cladosporioides were restricted to the substomatal chambers, and this species did not colonize internal leaf tissue. Infections of A. alternata were also localized in the substomatal chamber, frequently with an intercellular colonization of the mesophyll tissue.