Abstract: Endophytic fungi play an important ecological role in promoting growth and alleviating environmental stress of host plants. In this study, we investigated the diversity and community composition of endophytic fungi isolated from the common reed in wetlands of the Yellow River Delta. A total of 318 endophytic fungal isolates were obtained from 1350 tissue (leaf, stem, and root) fragments and from three tidal zones with different soil salinity levels. rDNA ITS regions of these isolates were PCR amplified, sequenced, and phylogenetically analyzed. All the sequences were divided into 12 operational taxonomic units (OTUs) at the 98% similarity threshold. Ascomycota was found to be the most abundant flora at the level of the phylum and distributed in all tissues and sites. There were generally richer OTUs in roots than in leaves and stems, and leaves and stems shared the same OTU numbers. All the OTUs retrieved from leaves appeared in roots. The supra tide (low salinity zone) had the most OTUs among the three sampling sites, followed by high tide. Furthermore, the roots had the highest richness and diversity, whereas the leaves had the lowest; supra tide held the highest richness, and the middle tide had the highest diversity. Although unique OTUs could be found in different tissues and tidal zones of different salinity, the communities of culturable endophytic fungi were not substantially different among tissues or tidal zones (ANOSIM, P>0.05). Alternaria sp. was the shared dominant taxa among all samples.