We have performed an N-glycoproteomic analysis of the green microalgae Botryococcus braunii, a promising candidate for the production of biofuels, accumulating considerable amounts of hydrocarbon oils. Thereby, three different strains have been compared: Showa (Race B), AC761 (Race B) and CCALA778 (Race A) which differ in the type of produced hydrocarbons. In total, 517 unique N-glycosylated peptides have been identified analyzing intact N-glycopeptides as well as deglycosylated, 18O-labeled peptides. Intact N-glycopeptides that harbored N-acetylhexosamine (HexNAc) at the non-reducing end were identified. Surprisingly, these GnTI-dependent N-glycans were also found to be modified with (di)methylated hexose. This type of methylated GnTI-dependent N-glycans has not been described so far.