In this work, the brown algae Macrocystis pyrifera were pretreated with dilute sulfuric acid, water and three different types of ionic liquids (ILs): 1-ethyl-3-methylimidazolium acetate ([EMIM][OAc]), 1,5-diazabicyclo[4.3.0]non-5-ene acetate ([DBNH][OAc]) and 1,8-diazabicyclo-[5.4.0]–undec-7-ene–sulfurdioxide–monoethanolamine (DBU–MEA–SO2–SIL), to disassemble the complex polysaccharide structure. After each pretreatment procedure, enzymatic saccharification was performed to release the monosaccharides. The main building blocks of M. pyrifera were processed by derivatization via acid methanolysis and subjected to gas chromatographic analysis. It was found that the main constituents were alginate (60.6 wt.%) and cellulose (22.6 wt.%) of total carbohydrate content. The degradation of alginate requires the action of alginate lyase and oligoalginate lyase, which hydrolyze the main chain in a synergistic mechanism releasing uronic acid (unsaturated uronate). Upon saccharification of cellulose, cellulases and β-glucosidase were used allowing the release of glucose. It was found that the best pretreatment strategy for M. pyrifera consisted of a pretreatment with 2 vol.% sulfuric acid, followed by saccharification of cellulose with a mixture of cellulases at pH 5.2 for 4 h at 50 °C or by saccharification of alginate with the enzyme lyase/oligoalginate lyase at pH 7.5 for 2 h at 37 °C. The process resulted in a release of 68.4 wt.% of glucose (55.74 ± 0.05 mg glucose/g algae) whereas in the case of alginate 85.8 wt.% of uronic acid (193.7 ± 10.6 mg uronic acid/g algae) was released. To the best of our knowledge this is the first time that saccharification of both cellulose and alginate from brown algae is reported.