Abstract:[Objective] The populations of endophytic fungi from halophyte Suaeda heteroptera Kitag. grown in the salt flats in Shuangtaizi Estuary of Panjin, Liaoning province, China, were investigated. [Methods] Endophytic fungi were isolated and purified from the roots, stems and leaves of Suaeda heteroptera Kitag. with traditional method. Isolates were identified based on morphological, physiological and biochemical characteristics and rDNA-ITS sequence analysis. [Results] Overall, 49 endophytic fungi strains were isolated and purified, these strains were classified into 13 different genera, in which Glomerella, Alternaria, Colletotrichum and Cladosporium were dominant genera. The distribution of endophytes of host plants have some degree of tissue preference, and though there was not significant difference of the abundance level in different habitats, habitat specificity of some endophytic fungi communities was presented. [Conclusion] Our results suggested that Suaeda heteroptera Kitag. have abundant resouces of endophytic fungi, the species diversity of endophytic fungi communities is affected both by its host preference and by its different habitats.