The diversity and frequency of leaf endophytic fungi occurring in naturally regenerating and planted stands of manuka were investigated at several sites. A restricted and characteristic range of species was isolated from all sites, although marked differences were noted between natural and planted stands. In natural stands a Phyllosticta species was the single dominant endophyte. This fungus appears to be host species specific, as it was not isolated from the closely related kanuka (Kunzea ericoides) in mixed, even-aged stands of manuka and kanuka. The frequency of the Phyllosticta sp. fluctuated greatly between individual trees across single stands. No obvious environmental or other gradients were recognized which could explain this patchy distribution. The Phyllosticta sp., along with the two next most common species in natural stands, Diploceras leptospermi and an unidentified coelomycete, were absent from most of the planted stands sampled, and at very low frequencies when present. Although several of the planted stands were close to natural stands and had been established for several years, the difference between them has been maintained. The most common endophytes in planted stands were Botryosphaeria and Alternaria spp. These species, found at low levels in natural stands, are likely to be ‘opportunistic’ endophytes. They are probably also characteristic of the epiphytic mycota, invading only the living leaves of plants under stress. The difference in leaf endophyte communities between planted and natural stands of manuka may be an indication of wider differences in the microbial communities of the respective stands, and could prove significant for site restoration projects. Such projects using nursery-raised manuka plants as a pioneer species may be establishing stands lacking much of the natural diversity of manuka communities for extended periods following establishment.