ABSTRACT: Measurements of the efficiency of photosystem (PS) II have become widespread in biological oceanography, and various forms are used to assess the ‘health’ of marine phytoplankton and to help estimate primary productivity. Absolute values of PS II efficiency depend to some extent on the measuring system, but changes in PS II efficiency are most commonly interpreted in terms of cellular acclimations to changing irradiance (including photoacclimation and photoinhibition) and nutrient availability (especially N and Fe). Recent measurements of phytoplankton viability in the surface ocean have revealed that in many regions phytoplankton assemblages may contain large proportions of dead cells. The effect of these dead cells on apparent PS II efficiency is largely unknown. By mixing live and dead cells and measuring PS II efficiency, we show that the presence of photosynthetically non-functional (dead) cells has surprisingly little effect; in a number of species, mixtures in which 50% of the cells were dead had values of 0.5, similar to values often found in natural assemblages. A simple model indicates that the non-linear nature of the fluorescence ratio is responsible for this unexpected result. We conclude that relatively high values of PS II efficiency cannot be used as evidence of low mortality. Our findings highlight the need for more information on the physiological status of both eukaryotic and prokaryotic microalgae in nature.