Effectiveness of microwave irradiation was demonstrated for hydrolysis of Ulva spp. with addition of polyoxometalate (POM) clusters. Aqueous solution of POMs (2–50 mM) at 140 °C yielded 349–435 mg g⁻¹ of neutral sugars (predominantly constituted of rhamnose) and uronic acids from Ulva spp. under an electromagnetic field. POMs were also capable of producing significantly larger amounts of reducing sugars than hydrochloric and sulfuric acids by 1.67–6.27 times with only very low amount of furfural derivatives (≤0.1%). Phosphotungstic acid (PW) was found to be the most suitable POM for hydrolysis of Ulva spp. Microwave irradiation showed higher production of sugars than external conduction heating using an induction oven by 5–10% (neutral sugars) and 24–33% (uronic acids) at the same thermal history. In addition, PW was recycled at least three times by diethylether extraction without changing its activity.