Different stages of the automortality in phytoplankton have been studied applying flow cytometry. These stages are, in order of expression: (1) compromised cell membranes, (2) degradation of the photosynthetic pigments and reduction of the photosynthetic activity, (3) fragmentation of the genomic DNA. The integrity test of the cell membranes is based on the inability of the DNA-specific stain SYTOX Green to pass into cells with intact plasma membranes. The reduction in photosynthetic activity was examined by sorting 14C-labelled phytoplankton cells differing in viability. Finally, DNA fragmentation was traced by measuring changes in genomic DNA. The different phytoplankton species tested showed a great variety in response when grown under the same conditions, but there was also considerable intraspecific variation. Unstained cells, fully stained cells (equivalent to full staining of genomic DNA in fixed cells) and cells with intermediate fluorescence signal occurred together within the same culture. The photosynthetic activity in cells with a reduced viability dropped by as much as 60% relative to that of the viable cells. In the subsequent stage, when photosynthetic pigments were fully degraded, this value dropped further to around 10%. Cells in this stage also showed subdiploidy as a result of genome fragmentation. Field tests using samples of phytoplankton collected in the North Atlantic Ocean (40° N, 23° W) during spring showed staining properties similar to those found in cultures grown at suboptimal growth conditions. The percentage of non-viable cells varied considerably (ranging from 5% to 60%) between the various phytoplankton groups present. The lowest value was observed for Synechococcus, but some pico-eukaryotes showed percentages as high as 60%. Moreover, the viability varied with depth (light level) and over a light–dark cycle. The present findings suggest the existence of a (genetically based) uniform process of automortality in phytoplankton. Non-viable cells are a substantial component of the oceanic phytoplankton, affecting the food-web structure and species succession.