Abstract: Water has always been a resource in absence in the Middle East. Water for agriculture, of different origins and quality is used in the Israeli orchards. One of the major water resources for citrus orchards in Israel is treated waste water. Long term irrigation with waste water influence trees health and appearance. It is clear that the water quality plays a major role in the trees health as well as fruit quality and quantity. Many possible explanations for the trees deterioration have been suggested, among them soil physical character changes, plants root damage and root associated microbial community changes. We suggested another, different approach, claiming that high concentrations of solubles in the treated water are changing the endophytes communities in the tree tissues. These changes cause the loss of beneficial endophytes aiding the trees. We have sampled trees from two orange orchards different only by the water used for their irrigation. Both orchards are of the same citrus variety and stock, planted on the same type of soil and climatic area. Fungal endophytic communities among samples from the two watering were compared using two methods; by isolation of fungi from the different tissues and Next Generation Sequencing (NGS). Samples were collected from roots, branches and leaves at summer, fall, winter and spring. All samples (72 samples) were used for fungal endophytes isolation and total DNA extraction. Phenotypic characterization and ITS identification were done to isolates from the different samples. Deep sequencing of all samples was performed by amplification of a 28S rRNA LSU sequence (LROR/LR3) of the fungal endophytic communities. Data was generated by MiSeq technology analysed using QIIME program. Ribosomal Database Project (RDP) was used for taxa identification. Differences between the methods used, and among samples and treatments in fungal composition are observed. Demonstration of these differences, with emphasis on root tissue is presented.