Many phytoplankton produce methane, a potent greenhouse gas. However, little is known about the relationship between their methane production and photosynthesis, which drives carbon sequestration in the oceans. Here, by ruling out the possibility of classical methanogenesis, we show that the bloom-forming marine microalga Emiliania huxleyi released methane during photosynthesis (did not generate it in darkness) while grown under different light levels, the amount of methane released correlated positively with photosynthetic electron transfer and carbon fixation. Under growth-saturating light, E. huxleyi produces methane at a maximal rate of about 6.6 ×10−11 μg cell−1 d−1 or 3.9 μg g−1 particulate organic carbon d−1. The microalga released up to 7 moles methane while fixing about 105 moles of carbon dioxide. Considering the higher global warming potential of methane than that of carbon dioxide and complicated processes involved in methane air-sea fluxes, the warming potential of phytoplankton methane production should be broadly evaluated. Phytoplankton Emiliania huxleyi produce methane during photosynthesis, which may counteract their carbon sequestration potential, according to lab experiments on cultured phytoplankton. Here, by ruling out the possibility of classical methanogenesis, we show that the bloom-forming marine microalga Emiliania huxleyi released methane during photosynthesis (did not generate it in darkness) while grown under different light levels, the amount of methane released correlated positively with photosynthetic electron transfer and carbon fixation. Under growth-saturating light, E. huxleyi produces methane at a maximal rate of about 6.6 ×10 −11 μg cell−1 d−1 or 3.9 μgg −1 particulate organic carbon d−1. The microalga released up to 7 moles methane whilefixing about 105 moles of carbon dioxide. Considering the higher global warming potential of methane than that of carbon dioxide and complicated processes involved in methane air-sea fluxes, the warming potential of phytoplankton methane production should be broadly evaluated. The methane (CH4) mixing ratio in the atmosphere has increased from 715 ppbv in the preindustrial era to around 2000 ppbv at present1.C H4 traps more heat per molecule than carbon dioxide (CO 2) ,y e ti th a sas h o r t e r atmospheric lifetime (half-lifetime ca. 10 years), making its global warming potential ~80-fold more powerful than CO 2 during thefir s t2 0y e a r sa f t e ri t is released, and about 30-fold higher over the course of a century2.T h u s ,C H4 is the second most important source of anthropogenic greenhouse gas fol- lowing CO 2. Consequently, understanding the sources and sinks of CH4 in the marine realm is essential for projecting the magnitude of future global warming and exploring mitigation solutions for the remediation of short- lived greenhouse gases. Vast amounts of CH 4 are produced in the oceans. Yet, the proportions of CH4 released from the oceans to the atmosphere have traditionally been considered minor3,4. hux- leyi,w ef o u n dt h a tC H4 production increases proportionally with photo- synthetic electron transfer and carbonfixation under illumination, with no CH4 release detected in the darkness. Ourfindings allowed us to establish the CH 4 production quotient (MPQ), e xpressing the quantity of CH 4 released versus that of CO2 fixed by photosynthesis. Considering the higher global warming potential of CH4, this parameter established for different CH4-generating phytoplankton species may be utilized in estimating the counteractive role of phytoplankton CH4 production to photosynthetic CO2 removal via the marine biological CO2 pump in both laboratory and in situ observations. Since we ruled out disturbances from metha- nogenic archaea and heterotrophic bacteria in the cultures (Supplementary F i g s .6 ,7 )a n df o u n dt h a tE. huxleyicultures did not produce CH 4 in the dark (Fig. 3a), it is obvious that the CH 4 produced in the microalgal culture is directly linked to photosynthesis. The established methane production quotient (MPQ: molar CH 4 released vs molar CO2 fixed) (Fig.4d) based on the simultaneous measurement of CH4 production and Cfixation indicates that E. huxleyican release up to 7 CH4 moles whilefixing 105 moles of CO2. Changes during the 12 h light period in photosynthetic carbon fixation rates ( a), CH4 pro- duction rates ( b), and algal cell diameters ( c)o f E. huxleyi cultures as measured every 3 h. Calculated CH4 production quotients (the ratio of CH4 released to CO2 fixed) for cultures grown at 100 and 200μmol photons m−2 s−1 (d) (error bars mark the standard deviation for triplicate cultures). The asterisks and letters above the bars mark statistically signi ficant (p < 0.05) differences between the treatments. https://doi.org/10.1038/s43247-024-01860-3 Article Communications Earth & Environment | (2024) 5:695 4 subsequent upwardflux of CH4 to the atmosphere48, although little has been documented on these aspects28,49. CH4 produced from autotrophs may, to some extent, offset their contribution via photosynthetic CO2 fixation to the marine biological car- bon pump (BCP). The CO 2 fixed by phytoplankton photosynthesis and associated CH4 release may alter concentrations of CO 2 and CH4 in the upper oceans, which may affect theirfluxes to the atmosphere (Fig.6). To the best of our knowledge, this study is the only one so far to quantify CH4 production quotients (MPQ). Provided that different E. Methane production by three widespread marine phytoplankton species: release rates, precursor compounds, and potential relevance for the environment. Biogeosciences 16, 4129–4144 (2019). 28. Klintzsch, T. et al. Effects of temperature and light on methane production of widespread marine phytoplankton. J. Geophys. Res. Biogeosci 125, e2020JG005793 (2020). 29. Bi žić, M. Phytoplankton photosynthesis: an unexplored source of biogenic methane emission from oxic environments. J. Plankton Res. 43, 822–830 (2021).