Protoceratium reticulatum as a producer of yessotoxin (YTX) and its analogues is common in several coastal environments. The YTX‐producing strain of P. reticulatum, isolated from the German Bight (North Sea), was analysed to study toxin production under various autecological conditions. Experiments were carried out to investigate the influence of N/P ratio (2.44, 24.36 and 243.65), temperature (15 and 20 °C), salinity (5, 10, 15, 20, 25 and 30 ‰ salinity) and growth phase on YTX formation, cell size and chlorophyll a concentration. P. reticulatum showed the highest growth at 15 °C and higher salinities (25 and 30 ‰ salinity). In particular, higher temperature led to a reduced growth. The total YTX concentrations were higher at lower temperature. However, a clear correlation between salinity and YTX production was not observed at lower temperature. Furthermore, P‐limited and control cultures exhibited the highest cell quota of YTX at the end of the stationary phase; a dramatic effect occurred at 15 °C under P‐limitation, when the toxicity increased to ten fold higher values. Slight variations of the composition of the YTX analogues under nutrient limitation were observable. In addition, the results indicate that N‐limitation cause a lower cell size, whereas P‐limitation leads to a higher cell size; an influence of the salinity on cell size was also observable.