In dense stratified systems such as microbial mats, photosynthesis and respiration are coupled due to a tight spatial overlap between oxygen-producing and -consuming microorganisms. We combined microsensors and a membrane inlet mass spectrometer with two independent light sources emitting in the visible (VIS) and near infrared (NIR) regions to study this coupling in more detail. Using this novel approach, we separately quantified the activity of the major players in the oxygen cycle in a hypersaline microbial mat: gross photosynthesis of cyanobacteria, NIR light-dependent respiration of Chloroflexus-like bacteria (CLB) and respiration of aerobic heterotrophs. Illumination by VIS light induced oxygen production in the top approximately 1 mm of the mat. In this zone CLB were found responsible for all respiration, while the contribution of the aerobic heterotrophs was negligible. Additional illumination of the mat with saturating NIR light completely switched off CLB respiration, resulting in zero respiration in the photosynthetically active zone. We demonstrate that microsensor-based quantification of gross and net photosyntheses in dense stratified systems should carefully consider the NIR light-dependent behaviour of CLB and other anoxygenic phototrophic groups.