Marine algae are promising third-generation feedstocks for bioethanol production as they are fast growing, require minimal inputs, and do not compete for land. However, marine algae have complex cell walls which necessitate pretreatment prior to fermentation, and this represents a major component of the cost of bioethanol production. Standard pretreatment processes using acids are costly and generate hazardous waste streams. This study aims to develop an economic and environmentally friendly pretreatment process using ozonolysis for the marine algae Kappaphycus alvarezii and Gelidium amansii. Acid and ozone pretreatments were compared across the pretreatment, enzyme hydrolysis, and fermentation stages of bioethanol production. Acid pretreatment outperformed ozonolysis over the pretreatment and enzyme hydrolysis stages. However, it also generated as by-products the compounds 5-hydroxymethyl furfural (5-HMF) and levulinic acid (LA), which inhibited ethanol fermentation and reduced the efficiency of the process overall. Ozone pretreatment did not produce these inhibitory compounds, and as such outperformed acid pretreatment across the process as a whole. These results indicate the potential of ozonolysis as an economic and environmentally friendly pretreatment for the production of bioethanol from marine algae.