In recent years, interest in the use of microalgae as cell factories to produce biopharmaceutical glycoproteins increased observably. Microalgae often produce biopharmaceutical glycoproteins through post-translational modification of proteins via N-glycosylation. The biophysical properties of biopharmaceutical glycoproteins such as folding, stability, and molecular recognition are influenced by the N-glycosylation process. Hence, to better understand the activity and function of biopharmaceutical glycoproteins there is a need for comprehensive knowledge on the mechanisms and pathways of N-glycosylation in microalgae. In this study, whole genome databases of different microalgae were assessed for the presence as well as the evolutionary relationship of putative Golgi glycosyltransferases (GTs) and glycosidases (GSs) using comprehensive bioinformatic techniques. The results showed that the presence and number of GTs, GSs, and mature N-glycan structures were organism specific. Since GTs and GSs had complex phylogenetic trees and conserved motif architectures, they potentially had complex evolutionary relationships and diverse functions in different organisms. Microalgal and human N-glycosylation pathways were highly distinct, and this indicated that many efforts must be made to produce humanized biopharmaceutical glycoproteins in microalgae. Hence, genetic engineering approaches were proposed for five different microalgae to remodel the N-glycosylation into human-compatible N-glycans. All in all, the bioinformatic analysis and the proposed genetic engineering in microalgae are essential for the future in producing functional pharmaceutical proteins with humanized N-glycosylation.