Plants are now known to have mutually beneficial relations with various endophytic fungi; also, some fungi that grow similarly within plants may be facultative pathogenic or slightly deleterious. Both shoots and roots harbour independent groups of endophytes; in Ericaceous plants, there is some overlap between ericoid mycorrhiza-formers and endophytes. Our aim is to characterize endophytes and endophyte-like fungi in important elements of the natural vegetation of the Netherlands, particularly in protected ecosystems such as oak forests and heaths, and to gain insight into whether these endophytes are beneficial, neutral or deleterious. One ongoing project aims at characterizing the endophytic elements of ascomycete communities in Quercus robur leaves throughout the growing season and the period after the leaves are shed. Classic techniques are used for endophytic isolations and isolation from fruiting bodies, while direct molecular methods such as direct PCR and sequencing as well as DGGE are compared. Another project concerns root-inhabiting fungi of Ericaceae. At least two molecularly confirmed new taxa have been discovered, one of which, a new Cryptosporiopsis species, has been demonstrated as forming ericoid mycorrhizae that result in improved host growth.