To simplify a production system of hydrogen, to improve the production efficiency of the hydrogen and to enable the hydrogen to be mass-produced and/or to be industrialized in the production of the hydrogen by using microorganisms.

The hydrogen is produced by the microorganisms through a step for obtaining an assimilation source for the hydrogen formation by minute algae having a photosynthesis activity under a condition of ≥5.0 atm osmotic pressure of a liquid phase under a light aerobic condition, and a step for synthesizing the hydrogen by using the assimilation source under a dark anaerobic condition by bacteria having the photosynthesis activity. The minute algae and bacteria having the photosynthesis activity are put in a liquid and used in a state immobilized on a carrier insoluble to the liquid. The bacteria having the photosynthesis activity are preferably used in a state in which a nitrogenase is preferably induced at a high activity. Carbon dioxide in a gas phase in the process through the assimilation of the hydrogen production by the minute algae having the photosynthesis activity is preferably regulated so as to be in a high concentration of 1.0-20.0%.