Endophytic Aspergillus Fumigatus sp. LH02, isolated from the roots of soybean and indentified through phylogenetic analysis of 18S rDNA sequence, was found stimulatory to the growth of Waito-C rice seedlings among 13 other endophytic strains screened. In growth hormone analysis, pure culture of fungal isolate produced three gibberellins viz GA4, GA9 and GA12. To know the role and effect on soybean in endophytic association (EA) and non-endophytic association (NEA) under salt stress (70 and 140mM), experiment was carried out at growth chamber using complete randomized block design. The results elaborated that the EA has significantly increased the shoot length, shoot and root fresh and dry weights, chlorophyll content, photosynthesis rate and leaf area of the plants with and without salt stress compared to control. Field emission scanning electron microscope analysis of root's surface showed that EA plants were extensively colnized by Aspergillus fumigatus LH02 under high salanity. In phytohormonal anlysis, ABA contents in EA and NEA were almost similar. Howere, when plants were exposed th salt stress, ABA levels were found significantly low in EA compared to NEA plant. In isoflavone content analysis, aglycones, malonyl, acetyl and glucosides isoflavones (total 11 compounds) were analyzed for each treatment through extensive HPLC andalysis. The quantities of isoflavone were found higher in EA plant's leaves with and without salt stress compared to NEA plant leaves. In conclusion, such endophytic association can be beneficial to explore ways to improve crop production under stressful conditions.