Iran with large saline areas is an ideal habitat for growth of plants of the family Chenopodiaceae. Diversity, frequency, and population density of endophyte fungi species depend on the edaphic and climatic conditions, heterogeneity of habitats and niches present within the host tissues, as well as on the competing organisms. In order to isolate endophytic fungi, 52 specimens of each Chenopodiaceae species were collected from its natural habitats in dry and temperate ecosystems located in the south and north of Iran. Staining roots showed that hyphae, spore and microsclerotia of endophytes are present in all surveyed roots. After surface disinfection, specimens were cultured on potato dextrose agar medium (PDA). A total of 192 fungal isolates were obtained and identified on the basis of morphological features and molecular identification. Obtained isolates consisted of eight dematiaceous genera (Alternaria, Bipolaris, Chaetomium, Cladosporium, Curvularia, Embellisia, Macrophomina and Ulocladium) and four non dematiaceous genera (Acremonium, Aspergillus, Fusarium and Penicillium) and twelve types of sterile mycelia. We isolated three species of Alternaria in the studied sites that base on phylogenetic studies located in three different groups. Most of plant roots had a colonization rate of 100% in dry ecosystems (site A, B), while the average colonization rate in temperate ecosystem was 63.8%. However, Shannon's and Fisher's Alpha indices indicate diversity of fungi in temperate ecosystem (site C, 2.45) is higher than that of in other sites. Among the genera, Fusarium was the most abundant in all ecosystems (site A 51%, site B 49% and site C 57%). Climate and soil condition can alter frequency of endophytic fungi in each ecosystem, so that site C with different altitude and soil condition in temperate region had different fungal distribution patterns compared to other studied sites in arid region. Our observations showed that higher endophytic fungi frequency can occ
