Hydrogen is a green and sustainable energy source due to its combustion process that only produces water and no carbon emissions. Microalgae have gained attention for their potential in biohydrogen production, as their biomass can be obtained by growing in wastewater which removes nutrients and fixes carbon dioxide in open/close culture systems. Biohydrogen can be produced from microalgae through fermentation, bio-photolysis, and bio-electrochemical methods. Microalgae-based biohydrogen production processes have advantages and limitations and are affected by factors such as light, temperature, and environmental pH. Low hydrogen production, the oxygen sensitivity of hydrogenase enzymes, and high production costs are the main challenges in hydrogen production from microalgae. To address the drawbacks and increase hydrogen production, different genetic and metabolic engineering approaches have been employed. Using innovative technologies such as bio-electrochemical systems or the integration of different techniques could be a novel strategy for developing and upscaling microalgae-based hydrogen production.