The physiology of the environmental bacterium Cupriavidus metallidurans CH34 (previously Ralstonia metallidurans) is being studied in comparison to the clinical model bacterium Escherichia coli in order to understand its behaviour and resistance under extreme conditions (e.g. space biology). In order to estimate physiological changes associated with pH stress, flow cytometry was employed to estimate the extent of damage on cell size, membrane integrity and potential and production of superoxides in the two bacterial strains. C. metallidurans and E. coli were submitted to a pH stress. C. metallidurans cells exhibited a different staining intensity than E. coli cells. For both bacterial strains, the physiological status was only slightly affected between pH 6 and 8 in comparison with pH 7 which represents the reference pH. Moderate physiological damage could be observed at pH 4 and 5 as well as at pH 9 in both strains. At pH 2, 10 and 12, membrane permeability and potential, esterase activity, intracellular pH and production of superoxide anion production were increased to high levels showing dramatic physiological changes. Flow cytometry is useful and complementary for monitoring physiological changes induced not only by pH stress but also for space stress.