Surfaces of marine macrophytes (seagrasses and macroalgae) are inhabited by diverse microbial communities. Most studies focusing on epiphytic communities of macrophytes did not take into account temporal changes or applied low sampling frequency approaches. Illumina sequencing of the V4 16S rRNA region was performed to determine the seasonal dynamics of epiphytic communities of the seagrass Cymodocea nodosa and invasive macroalga Caulerpa cylindracea. Leaves and thalli were sampled in a meadow of Cymodocea nodosa invaded by the invasive Caulerpa cylindracea and in a monospecific settlement of Caulerpa cylindracea located in the proximity of the meadow at monthly intervals. For comparison the ambient prokaryotic plankton community was also characterized. At the OTU level, the microbial community composition differed between the ambient water and the epiphytic communities exhibiting host-specificity. Also, successional changes were observed connected to the macrophyte growth cycle. Taxonomic analysis, however, showed similar high rank groups in the ambient water and the epiphytic communities, with the exception of Desulfobacterota, which were only found on Caulerpa cylindracea. Cyanobacteria showed seasonal changes while other high rank taxa were present throughout the year. Phylogenetic groups present throughout the year constituted most of the sequences, while less abundant taxa showed seasonal patterns connected to the macrophyte growth cycle. Taken together, epiphytic microbial communities of the seagrass Cymodocea nodosa and the macroalgae Caulerpa cylindracea appear to be host-specific and contain taxa that undergo successional changes.