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The photosynthetic quotient (PQ) is defined as the molar ratio of oxygen released to the carbon dioxide assimilated during photosynthesis. Calculation of correct PQ values of natural phytoplankton populations is crucial for understanding of carbon budgets but often result in values that differ highly from the expected stoichiometric proportions of photosynthetic products. In the present study, measurements of primary production, that is, CO2 assimilation, performed with the standard isotopic method (14C) and oxygen release estimated during photosynthesis with the light-and-dark bottle method were compared to calculate PQ in the southern Baltic (Gulf of Gdańsk, Poland). The PQ average was 1.28 (ANOVA; F = 872; R2 = 0.92; n = 77; p < 0.001). Neither nitrogen source nor phytoplankton composition was noted to impact PQ values. Very high PQ values in the lower range of production rates (that cannot be explained by the stoichiometric proportion of photosynthesis products) were interpreted as artifacts related to the lower sensitivity of the oxygen method compared to that of the 14C method.