Aquatic ecosystems are a significant source of methane emissions. Although methane production has previously been recognized to only occur in oxygen-deprived environments, recent research has shown that aerobic water environments also experience high methane levels, known as the “methane paradox”. This phenomenon is linked to the presence of algae that can directly produce methane through photosynthesis or the use of specific compounds. Moreover, algae create conditions conducive to methane production by other microorganisms. However, the specific ecological mechanism of aerobic methane production by algae remains not yet fully understood, making accurate global methane level accounting difficult. Future studies should focus on uncovering the molecular regulation of aerobic methane production by algae and how they adapt to external conditions.