Pinoresinol diglucoside (PDG) is the important antihypertensive compound in Eucommia ulmoides Oliv., a traditional Chinese herb medicine. The research objective was to certify the possibility of producing PDG through fermentation. PDG-producing endophytic fungi were isolated from E. ulmoides Oliv., and the highest PDG-yielding (11.65 mg/L) isolate, XP-8, was identified as Phomopsis sp. according to the morphological characteristics and the phylogenetic tree constructed on the basis of the gene sequence in the internal transcribed spacers district. The microbial PDG was isolated by using S-8 resin and purified to a purity of 98.7% using preparative high-performance liquid chromatography (HPLC). Information obtained from the UV spectrum (277 and 227 nm, in water solution), infra-red spectrum (3,428; 2,930; 2,877; 1,637; 1,600; and 1,513; 1,460; 1,421; 1,269; 1,223; 1,075; 658 cm(-1), in powder), molecular weight (682 Da, measured using HPLC-electrospray ionization mass spectrometry (ESI/MS) and tandem mass spectrometry), and nuclear magnetic resonance analysis show the microbial PDG is (+)-1-pinoresinol 4,4'-di-O-β-D-glucopyranoside, same as the plant-derived PDG. The microbial PDG is stable in pH range from 3 to 11 but less stable at temperature higher than 90 °C and in light exposure. During the fermentation, PDG production outside cells starts at the later stage of cell growth when the residual sugar in the medium was low. The study reveals the possibility for production of PDG by fermentation.