To identify reference strain CMCC(F)98003, which cited in Chinese Pharmacopoeia (CHP), polyphasic approaches including morphological features, Biolog identification system, ITS rDNA sequence, specific positions based on the ITS region and β-tubulin gene sequences analysis were used. Results indicated that CMCC(F)98003 was identified as Aspergillus niger and consistent with the scientific name in CHP. Although A. brasiliensis is close to A. niger, they have been classified as two different species and their morphology, phylogenesis and metabolic profilies are distinct. To maintain the consistency of international Pharmacopoeia, whether CHP replaces the new representative of filamentous fungi strain is worth studying.