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1. Foliar endophytic fungi in herbaceous plants are known to be diverse, yet studies characterizing the fungal communities in roots and shoots of plants across time are absent. These fungi are supposedly ubiquitous in nature, infecting plants through airborne spores. As many foliar endophytes can also exist in soil, we hypothesized that there would be a strong similarity between root and shoot endophytes in any given plant species and that differences between plant species would be greater than those between organs within a species. 2. Leaf and root fungal endophyte communities were assessed in field-collected plants of three co-occurring grassland forbs (Cirsium arvense, Plantago lanceolata and Rumex acetosa) in two contrasting seasons (winter and summer). The former two species are mycorrhizal, whilst the latter species is not so. 3. The highest fungal species richness was recorded from P.lanceolata with R.acetosa hosting the least endophyte diversity. Endophyte communities were more diverse in root than leaf tissues and in summer than in winter. Similarity of endophyte communities between different host plant species and organs within an individual host was very low. Negative correlations were found between mycorrhizal colonization and endophyte presence in the roots of C.arvense and P.lanceolata, suggesting some degree of antagonism or competition between the fungi. Consistent positive associations were found between the number of endophyte species in roots and shoots of plants. 4. Synthesis. In contrast to previous studies, the results show that many endophytes do not occur ubiquitously, but instead exhibit both plant and tissue specificity. There is a strong seasonal change in endophyte communities, but the differences between roots and shoots at any one time can be just as large. This dissimilarity suggests a lack of systemic growth by the fungi from one tissue to another. Mycorrhizas may interact negatively with other root endophytes, indicating that the latter should not be ignored in future mycorrhizal studies. We should begin to think of individual plants as ecosystems of interacting microbes, whose community is structured by plant genetics and environmental conditions, coupled with interactions between the microbes themselves.