The cyanobacterium Microcystis aeruginosa and the green alga Scenedesmus obliquus were incubated individually and together in the dark and under anaerobic conditions created by adding the reducing agent cysteine. Flow cytometry was used to monitor cell concentrations, fluorescence of chlorophyll-a (chl-a), and cell metabolic activity measured with an esterase-sensitive probe to detect fluorescein diacetate (FDA) hydrolysis of the two species. M. aeruginosa showed a slight increase in cell metabolic activity, no conspicuous death of cells, and absence of decay of chlorophyll-a fluorescence in individual and competition cases under dark anaerobic conditions. Cell metabolic activity and fluorescence of S. obliquus, on the contrary, decreased sharply, and cell concentrations fluctuated markedly with time in the unialgal cultures, but showed only a slight decline in the mixed cultures. M. aeruginosa appeared to be more tolerant to dark anaerobic conditions than S. obliquus, which may arise in eutrophic lakes beneath thick surface scums in the water column, or in the bottom sediments. Tolerance of these conditions may be important to the dominance of M. aeruginosa in eutrophic lakes.