Aerobic methane production by the marine diazotrophic cyanobacterium Trichodesmium erythraeum IMS101 has been documented and is stimulated by external supplies of methylphosphonate and increasing temperatures. Moreover, previous studies demonstrate that inhibition of the photosynthetic electron transport (PET) chain suppresses methane production under light conditions, suggesting a close association between PET and methane formation. Yet, the mechanisms underlying this methane production remain unknown. In this study, we investigated possible molecular foundations of photosynthesis-associated methane production in exponentially growing and photosynthesizing cultures of T. erythraeum IMS101throughout the diel cycle (12 h light–12 h dark). We combined physiological measurements including photophysiological parameters, carbon fixation and methane production with transcriptomic analyses obtained from extracted and sequenced RNA. We focused on metabolic pathways and possible genes whose transcription patterns may be specifically associated with methane production such as transcriptional changes in PET, chlorophyll catabolism, and photosynthetic C₁ metabolism, three metabolically interconnected pathways hypothesized to contribute to methane formation. This work aims to provide a transcriptome-wide characterization of the molecular basis of methane production in Trichodesmium grown on inorganic dissolved phosphorus (phosphate) and contribute to understanding some of the mechanisms and pathways contributing to photosynthesis-associated marine methane production.