A fungus identified as Aspergillus aculeatus was used to biotransform genistein and glycosides to polyhydroxylated isoflavones. The strain was identified on the basis of colony morphology features and ITS rDNA sequence analysis. Phylogenetic tree was constructed to determine its taxonomic status. Genistein and glycosides were transformed by Aspergillus aculeatus to 5,7,8,4’- tetrahydroxyisoflavone. The chemical structure of the product was identified by high performance liquid chromatography(HPLC), liquid chromatography-mass spectrometry(LC/MS), Infrared spectroscopy (IR) and NMR spectrometer methods. The ITS rDNA sequence of the strain had 100% similarity with Aspergillus. Furthermore, it was ultimately identified as Aspergillus aculeatus. The metabolite of genistein and glycosides was identified as 5,7,8,4’-tetrahydroxyisoflavone. 120 mg 5,7,8,4’-tetrahydroxyisoflavone was made from 20 g fructus sophorae, which was bioconverted unconditionally by Aspergillus aculeatus for 96 h, and the purity was 96%. On the basis of the findings, Aspergillus aculeatus was a novel strain with specific ability to convert genistein and glycosides into 5,7,8,4’-tetrahydroxyisoflavone which had potential applications.