Cyanobacteria are major primary producers in coastal microbial mats and provide biochemical energy, organic carbon, and boundnitrogen to the mat community through oxygenic photosynthesis and dinitrogen fixation. In order to anticipate the specificrequirements to optimize their metabolism and growth during a day-and-night cycle, Cyanobacteria possess a unique moleculartiming mechanism known as the circadian clock that is well-studied under laboratory conditions but little is known about itsfunction in a natural complex community. Here, we investigated daily rhythmicity of gene expression in a coastal microbial matcommunity sampled at 6 time points during a 24-h period. In order to identify diel expressed genes, meta-transcriptome data wasfitted to periodic functions. Out of 24,035 conserved gene transcript clusters, approximately 7% revealed a significant rhythmicexpression pattern. These rhythmic genes were assigned to phototrophic micro-eukaryotes, Cyanobacteria but also toProteobacteria and Bacteroidetes. Analysis of MG-RAST annotated genes and mRNA recruitment analysis of two cyanobacterial andthree proteobacterial microbial mat members confirmed that homologs of the cyanobacterial circadian clock genes were alsofound in other bacterial members of the microbial mat community. These results suggest that various microbial mat membersother than Cyanobacteria have their own molecular clock, which can be entrained by a cocktail of Zeitgebers such as light,temperature or metabolites from neighboring species. Hence, microbial mats can be compared to a complex organism consistingof multiple sub-systems that have to be entrained in a cooperative way such that the corpus functions optimally.