Endophytic fungi are little known for exogenous gibberellins (GAS) production and plant growth promotion under salt stress conditions. We isolated 13 endophytic fungi from soybean roots, which were screened on Waito-C rice for plant growth promoting capacity. Endophytic strain, GMH-1a exhibited maximum growth during screening and thus was investigated for GAs production and host plant interaction. GMH-1a was identified as a new strain of Aspergillus fumigatus sp. LH02 through phylogenetic analysis of 18S rDNA sequence. Analysis of GMH-1a culture filtrate showed presence of GA(4) (24.8 ng/ml), GA(9) (1.2 ng/ml) and GA(12) (9.8 ng/ml). Soybean plants inoculated with GMH-1a significantly increased shoot length, shoot fresh and dry biomass, leaf area, chlorophyll contents and photosynthetic rate under salt stress (70 and 140 mM) as compared to non-inoculated plants. GMH-1a inoculated plants had contained significantly lower endogenous abscisic acid (ABA) and elevated free proline, salicylic acid (SA) and jasmonic acid (JA) contents in comparison to their respective control treatments. Isoflavones, quantified through excessive HPLC analysis, showed that GMH-1a inoculated plants with/without salt stress contained higher isoflavones than non-inoculated plants and with/without NaCl stress. This novel endophytic fungus has reprogrammed soybean metabolism to improve plant growth and increase isoflavone contents under salt stress. (C) 2010 Elsevier Ltd. All rights reserved.