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Soybeans offer an abundant source of isoflavones, which confer useful bioactivities when existing in aglycone forms. The conversion of isoflavones into aglycones via fermentation of soybean products is often realized by &#946;-glucosidase, an enzyme produced by fungi. In this study, a filamentous fungus, <i>Clerodendron cyrtophyllum</i>, was isolated from root of <i>Clerodendron cyrtophyllum</i> Turcz, which was able to produce the highest activity of &#946;-glucosidase up to 33.72 U/mL at 144 h during fermentation on Potato Dextrose Broth (PDB). The obtained fungus was grown on isoflavones-rich soybean extract to produce genistein and daidzein, achieving the conversion rate of 98.7%. Genistein and daidzein were isolated and purified by column chromatography using hexane/acetone (29:1/1:1), reaching purities of over 90% of total isoflavones, as identified and determined by TLC, LC-MS/MS, and ¹H and ¹³C NMR spectroscopy. These results imply that the isolated <i>P. citrinum</i> is a potential fungal strain for industrial-scale production of genistein and daidzein from isoflavones-containing soybean extracts. These products may serve as potential raw materials for manufacture of functional foods that are based on aglycones.