Industrial strain of Aspergillus niger has been used to produce citric acid for almost one century and is currently the primary source of commercial citric acid production. This complex bioprocess is known to depend on both endogenous and exogenous factors. Those factors execute their effects on this complex bioprocess via regulation of gene expression and post-translational modification. One common post-translational modification is protein glycosylation. Protein glycosylation plays important roles in proper protein folding, stability, secretion and functions. It also involves in cell signaling, protein translocation and cell wall biogenesis. There exist two types of protein glycoylation: N-linked glycosylation on asparagines and O-linked glycosylation on serine/threonine. There are many enzymes involve in both N- or O-glycosylation pathways. In this study, several enzymes involving in the protein N-glycosylation were examined for the potential effects on fungal morphology and citric acid production via gene deletion in A. niger. The results from our study demonstrated that the deletion of Dolichyl-P-Man:Man(5)GlcNAc(2)-PP-dolichyl mannosyltransferase gene (alg3∆) significantly affect fungal morphology and enhance citric acid production in A. niger.