Abstract The hydrogen production in the cyanobacterium Synechocystis sp. strain PCC6803-GT in the dark anaerobic nitrate free buffer solution with or without monosaccharide has been studied by following the time courses of the amounts per culture volume of hydrogen, exogenous monosaccharide, endogenous glucose in glycogen, dry weight biomass, acetate, lactate and succinate. The monosaccharides utilized in this work were reducing sugars, which were glucose, fructose, galactose, mannose and xylose. The rate of hydrogen production was highest right after dark incubation. The early hydrogen production was always accompanied by the decomposition of endogenous glucose in glycogen in the absence of exogenous glucose, while it was accompanied by the assimilation of exogenous glucose in the presence of exogenous glucose. The amount of endogenous glucose was elevated under the condition where cells assimilated exogenous glucose. The analysis of metabolic product distribution results that the bulk of NAD(P)H and reductive flavodoxin/ferredoxin for hydrogen production on Ni-Fe hydrogenase is served by not only glycolysis but also by initial accumulation of those reductive compounds and decomposition of other cell constituting materials. The cells containing high amount of glucose in glycogen at the end of dark incubation showed high production of hydrogen. The amount of endogenous glucose was elevated by addition of exogenous glucose. Cell survival to stabilize the high level of endogenous glucose against dark nitrate free environment was supported by addition of fructose.