This paper describes the anaerobic digestion of microalgal biomass from high rate ponds in continuous anaerobic reactors for biogas production. With hydraulic retention times (HRT) of 15 and 20 days, the volatile solids (VS) removal did not exceed 30%, and the methane production rate ranged between 0.12 and 0.14 L CH4/L day. To improve process performance, microwave irradiation at 900 W for 3 min (specific energy ∼70,000 kJ/kg VS) was applied as a pretreatment step. The VS removal increased to 40 and 45% at 15 and 20 days HRT, respectively. Consequently, the methane production rate increased to 0.16 and 0.20 L CH4/L day at 15 and 20 days HRT, respectively. Microscopic analysis confirmed cell wall damage, although generally without lysis, after irradiating microalgal biomass. However, the energy consumption was much higher than the extra energy production of the process. Indeed, microalgal biomass should not only be thickened but also dewatered if microwave irradiation was to be applied as a pretreatment to anaerobic digestion for biogas production.