The anaerobic digestion, AD, process presents a solution for sustainable waste management, greenhouse gas mitigation and energy production for growing population needs and requirements. Adopting a biorefinery approach that utilises different feedstock may enhance energy production and support optimisation of the anaerobic digestion process. Algae is a promising feedstock that could be used for energy production via the anaerobic digestion process. Microalgal biomass is rich in carbohydrates and lipids; however, many species of algae exhibit tough cell walls that could also be difficult to digest and may influence or inhibit the efficiency of the AD process. This study concentrated on the comparison of AD remediation of two marine algal biomass species, Tetraselmis suecica and Nannochloropsis oceanica. The two species were pre-treated with an ultrasound technique and compared for their methane production using biochemical methane potential tests. For Tetraselmis, a specific methane production of 0.165 LCH4/KgVS was observed; however, for Nannochloropsis, a value of 0.101 LCH4/KgVS was observed for the samples treated with ultrasound. The BMP results from this study show that among the two micro-algae species tested, Tetraselmis suecica is found to be a better substrate for methane production potential. Contrary to increasing the specific methane production, ultrasound cavitation caused a slight decrease in the specific methane production values for both Nannochloropsis oceanica and Tetraselmis suecica biomass residues. The pre-treatment of the biomass using ultrasound techniques provided comparable results and can be recommended for effective bioenergy production. However, further research is required for the optimisation of the pre-treatment of microalgae and for the integration of microalgal biorefineries for circular economy.