The presence of seagrass shapes surface sediments and forms a specific environment for diverse and abundant sediment microbial communities. Although severe declines of seagrass meadows have been reported there is limited available data on the response of sediment communities to such an event. As Cymodocea nodosa represents a common seagrass species in the Mediterranean sea, no detailed characterization of its sediment microbial communities is available, and severe declines have been documented, sediment of a declining Cymodocea nodos meadow was sampled. In order to characterize and asses changes in microbial communities Illumina MiSeq sequencing of the V4 region of 16S rRNA was performed. Samples were collected from surface sediments at monthly intervals from July 2017 to October 2018. For comparison, samples from an adjacent nonvegetated area were also analysed. Microbial communities differed primarily by sediment depth and by the area sampled. Although the C. nodosa meadow declined to a point where almost no leaves were present no clear temporal community variation was observed. Taxonomic analysis showed a clear dominance of bacterial over archaeal sequences, with most archaeal reads classified as Nanoarchaeota, Thermoplasmatota, Crenarchaeota and Asgardarchaeota. The bacterial community was mainly composed of Desulfobacterota, Proteobacteria, Bacteroidota and Chloroflexi. Our results suggest that changing environmental conditions caused by the decline of a seagrass meadow do not have a strong influence on the sediment microbial community composition.